Method of making recombinant silk and silk-amyloid hybrid proteins using bacteria

ABSTRACT

Disclosed are methods of making recombinant secretion of silk and collagen proteins, and amyloid fusions thereof, using bacteria.

RELATED APPLICATIONS

This application is a continuation-in-part of U.S. application Ser. No. 15/776,998, filed May 17, 2018; which is the US national stage under 35 U.S.C. sec. 371 of Patent Cooperation Treaty Application No. PCT/US16/62820, filed Nov. 18, 2016; which claims priority to U.S. Provisional Application No. 62/257,405, filed on Nov. 19, 2015.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May Jul. 21, 2021, is named NEX-09502_SL.txt and is 845,639 bytes in size.

FIELD

The technology described herein relates to the engineering of a polypeptide secretion system, exogenous nucleic acids encoding a recombinant protein, proteins that include a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, engineered silk fibroin domains, and optionally amyloid-based extracellular matrix components produced by engineered bacterial cells.

BACKGROUND

Silks are protein fibers produced by arthropods. Large-scale production methods include cultivation of Bombyx mori silkworms. These silks are naturally used as a self-generated biomaterial by a wide variety of insects and are used for a diverse array of functions, such as anchoring and protection of eggs, lining of nests, binding agents for nest construction, sperm transfer, cocoon formation, and prey traps. Silk fibers possess properties of strength and elasticity that make them a highly valuable commodity. Spider silks are five times stronger on a per weight basis than steel and three times tougher than Kevlar®. Griffiths, J. R. & Salanitri, V. R. The strength of spider silk. J. Mater. Sci. 15, 491-496 (1980). It has a large extensibility and energy to breakage (toughness) exceeding that of most engineering materials. Gosline, J. M., Guerette, P. A, Ortlepp, C. S. & Savage, K. N. The mechanical design of spider silks: from fibroin sequence to mechanical function. J. Exp. Biol. 202, 3295-3303 (1999). It has also been reported that spider silk possesses a thermal conductivity 800 times greater than any other organic material. Huang, X., Liu, G. & Wang, X. New secrets of spider silk: Exceptionally high thermal conductivity and its abnormal change under stretching. Adv. Mater. 24, 1482-1486 (2012). Furthermore, spider silk undergoes supercontraction from temperature and pH changes. Guan, J., Vollrath, F. & Porter, D. Two mechanisms for supercontraction in Nephila spider dragline silk. Biomacromolecules 12, 4030-4035 (2011). However, since spiders are venomous and cannibalistic, they cannot be easily domesticated on a large scale for spider silk production.

Spider silk and other protein production has been explored in bacteria, yeast, plants, and mammalian cells. See Fahnestock, S. R. & Irwin, S. L. Synthetic spider dragline silk proteins and their production in Escherichia coli. Appl. Microbiol. Biotechnol. 47, 23-32 (1997); Xia, X.-X. et al. Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber. Proc. Natl. Acad. Sci. 107, 14059-14063 (2010); Widmaier, D. M. et al. Engineering the Salmonella type III secretion system to export spider silk monomers. Mol. Syst. Biol. 5, 1-9 (2009); Fahnestock, S. R. & Bedzyk, L. A. Production of synthetic spider dragline silk protein in Pichia pastoris. Appl. Microbiol. Biotechnol. 47, 33-9 (1997); Yang, J., Barr, L. A., Fahnestock, S. R. & Liu, Z.-B. High yield recombinant silk-like protein production in transgenic plants through protein targeting. Transgenic Res. 14, 313-24 (2005); Lazaris, A. Spider Silk Fibers Spun from Soluble Recombinant Silk Produced in Mammalian Cells. Science (80). 295, 472-476 (2002); Widmaier, D. M. & Voigt, C. a. Quantification of the physiochemical constraints on the export of spider silk proteins by Salmonella type III secretion. Microb. Cell Fact. 9, 78 (2010); Sivanathan, V. & Hochschild, A. Generating extracellular amyloid aggregates using E. coli cells. Genes Dev. 26, 2659-2667 (2012).

What is more, the occurrence of widespread diseases among animals that causes health problems inhibits the immense production and use of animal source proteins. As a consequence, recombinant proteins are emerging as the sources with lower immunogenicity and inflammation response compared to animal sources. Fertala, A. Three Decades of Research on Recombinant Collagens: Reinventing the Wheel or Developing New Biomedical Products? Bioengineering (Basel) 7. Collagen is among the most abundant proteins in animals that plays a major structural role in tissue formation. It is thus a protein of choice in different fields such as cosmetic, tissue engineering, and fabricating synthetic biomaterials. Radhakrishnan S., Nagarajan S., Bechelany M., Kalkura S. N., in Processes and Phenomena on the Boundary Between Biogenic and Abiogenic Nature. Lecture Notes in Earth System Sciences (ed Vlasov D. Frank-Kamenetskaya O., Panova E., Lessovaia S) (2010).

Bacterial collagen has been previously genetically modified and produced intracellularly in E. coli for biomedical applications. An, B. et al. The influence of specific binding of collagen-silk chimeras to silk biomaterials on hMSC behavior. Biomaterials 34, 402-412; Seo, N. et al. An engineered alpha1 integrin-binding collagenous sequence. J Biol Chem 285, 31046-31054; Peng, Y. Y. et al. A simple cost-effective methodology for large-scale purification of recombinant non-animal collagens. Appl Microbiol Biotechnol 98, 1807-1815. In such reports, cell lysis has been used as a necessary step for extracting of intracellular collagen. However, extracellular production of proteins has significant advantages compared to the conventional intracellular production, in both analytical and industrial scales. For instance, the product quality (e.g. biological activity and stability) of the expressed proteins in the culture medium is better preserved by their continuous secretion and protection from intracellular proteolysis by periplasmic proteases. Choi, J. H. & Lee, S. Y. Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol 64, 625-635. Further, intracellular systems demand cell disruption, which results in protein loss and contamination with host proteins. In contrast, an extracellular system is exempt from cell lysis, which consequently makes the purification process simpler and less costly. Su, L., Xu, C., Woodard, R. W., Chen, J. & Wu, J. A novel strategy for enhancing extracellular secretion of recombinant proteins in Escherichia coli. Appl Microbiol Biotechnol 97, 6705-6713. Accordingly, there is a tremendous need for protein-based materials that are derived from safe and biocompatible sources in the fields of biomaterials and tissue engineering.

SUMMARY

The present disclosure describes the use of a secretion system within a bacterium to secrete proteins, preferably collagen protein (e.g., bacterial collagen and domains thereof) or silk protein, such as a silk fibroin domain. The present invention is based, at least in part, on the use of an adapted secretion pathway, natively used by E. coli to secret curli fibers, for extracellular secretion of the bacterial collagen using only the essential signal peptides and curli operon genes for said secretion of collagen. Due to structural similarities with type I animal collagen, recombinant bacterial collagen-like proteins have been progressively used as a source of collagen for biomaterials applications. However, the intracellular expression and current time-consuming and costly chromatography methods for purification make the massive production of recombinant bacterial collagen challenging. Among the different types of the recombinant collagens, bacterial collagen-like proteins, such as Streptococcal collagen-like proteins, have a structure with mechanical and thermal stability comparable to type I animal collagen. Lukomski, S. et al. Identification and characterization of a second extracellular collagen-like protein made by group A Streptococcus: control of production at the level of translation. Infect Immun 69, 1729-1738, doi:10.1128/IAI.69.3.1729-1738.2001 (2001); Xu, Y., Keene, D. R., Bujnicki, J. M., Hook, M. & Lukomski, S. Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices. J Biol Chem 277, 27312-27318; Mohs, A. et al. Mechanism of stabilization of a bacterial collagen triple helix in the absence of hydroxyproline. J Biol Chem 282, 29757-29765. The biofunctionality of this type of collagen is tailorable and has been genetically modified to alter its biological activities by fusing functional protein domains, such as silk to the C-terminal end and single mutations to create integrin binding domains in the backbone of the bacterial collagen. An, B. et al. The influence of specific binding of collagen-silk chimeras to silk biomaterials on hMSC behavior. Biomaterials 34, 402-412; Seo, N. et al. An engineered alpha1 integrin-binding collagenous sequence. J Biol Chem 285, 31046-31054, each incorporated herein by reference in their entirety. Accordingly, such functionalization and modification as is known in the art (and/or in connection with silk peptides (e.g., fibroin domains) as disclosed herein), are contemplated.

Unlike animal collagen, bacterial collagen lacks hydroxyproline and cannot be post-translationally modified in bacterial cells. Despite these differences, it still forms a stable triple helix structure. Structurally, bacterial collagen consists of an N-terminal variable domain (globular domain, V′) attached to a rod-shaped collagen-like domain (helical domain, CL). A high content of proline and highly charged repeating sequences can be found near the C-terminal and N-terminal ends of the collagenous domain, which are key for structural stability of the bacterial collagen. Investigations in synthetic peptides have demonstrated that charged residues that are found in the X and Y positions of the triplet (G-X-Y) can promote electrostatic interactions and water-mediated contact between the charged side chains, which accordingly stabilize the triple helix structure. O'Leary, L. E., Fallas, J. A., Bakota, E. L., Kang, M. K. & Hartgerink, J. D. Multi-hierarchical self-assembly of a collagen mimetic peptide from triple helix to nanofibre and hydrogel. Nat Chem 3, 821-828; Fallas, J. A., Dong, J., Tao, Y. J. & Hartgerink, J. D. Structural insights into charge pair interactions in triple helical collagen-like proteins. J Biol Chem 287, 8039-8047.

One of the extracellular secretion pathways is natively found in Escherichia coli bacteria and serves for the secretion of CsgA proteins. CsgA is a self-assembling bacterial protein that is secreted inherently by E. coli and assembles into membrane-bound extracellular curli fibers. The structural components and assembly apparatus of CsgA consist of seven curli-specific genes (csg), which are encoded by two divergently transcribed operons (csgBAC and csgDEFG). These operons encode the structural subunit of the curli protein and other accessory proteins required for CsgA secretion and assembly.

In the curli secretion pathway, the SEC peptide and N22 peptide are two important components responsible for directing the secretion of CsgA into the periplasm and then across the outer membrane, respectively. These components are not specific to CsgA and are crucial for the extracellular secretion of other proteins through this pathway. The CsgE protein is known as a curli secretion specificity factor that prevents premature amyloid fibre aggregation, and, therefore, is crucial for the secretion of CsgA and CsgA fusion proteins, but also does not interfere with the secretion of proteins containing the N22 secretion signal peptide. Assisting CsgE, CsgF also takes part in the efficient curli assembly, and has been shown to interact with CsgG at the outer membrane. CsgG is an ungated, non-selective protein secretion channel that facilitates the leakage of periplasmic polypeptides via a diffusion-based transport mechanism. The CsgG transporter is capable of exporting heterologous and non-native sequences, amyloid or not, when fused to the curli subunit CsgA or a truncated form of CsgA. CsgC presumably has redox activity with CsgG being the potential substrate (FIG. 8A).

The extracellular production of proteins also indirectly permits their simplified purification, which is important for scalable manufacturing of biomaterials. In addition, establishing a low-cost simple purification technique represents an important engineering contribution for scalable manufacturing of protein-based materials. Specifically, there are several main drawbacks with current chromatography-based methods, such as high cost, low yield, limited sample volume, and protein loss due to metal ions leakage, which all will limit the massive production of the collagen. Therefore, in some aspects of the inventions, disclosed herein are purification protocols for isolating bacterial collagen, based on three main principles: the enzymatic digestion of the unwanted proteins by selectively cleaving proteins that are sensitive to proteases, the size-based separation of collagen via filtration, and the selective acid precipitation of collagen. Through precipitation and filtration, the large culture volumes can be processed and concentrated efficiently, facilitating collagen recovery. The non-specificity of the CsgG transporter provides an opportunity to exploit an existing system for extracellular secretion of the bacterial collagen.

According to certain aspects, a heterologous (e.g., an exogenous or foreign nucleic acid) encoding the silk or collagen protein is introduced into a bacterium. The bacterium can proliferate and express the nucleic acid to produce the silk or collagen protein which is also secreted by the bacterium. The silk or collagen protein may be secreted such that it is unattached from the bacterium and free of the bacterium or it may be attached to the outer surface of the bacterium, such as being a component of a curli fiber. According to one aspect, the silk or collagen protein comprises a periplasmic translocation signal sequence which facilitates the transport of the silk or collagen protein from the bacterial cytoplasm to the periplasm of the bacterium. According to one aspect, the silk or collagen protein comprises an outer membrane secretion signal sequence which facilitates the transport (e.g., export) of the silk or collagen protein to the extracellular milieu, i.e., through the outer membrane of the bacterium. According to one aspect, the silk or collagen protein comprises both a periplasmic translocation signal sequence and an outer membrane secretion signal sequence. In some embodiments, the periplasmic translocation signal sequence is cleaved off of the silk or collagen protein. In some embodiments, the outer membrane signal secretion signal sequence is cleaved-off the silk or collagen protein.

Embodiments of the present disclosure are directed to methods of genetically modifying a bacterium to comprise an exogenous nucleic acid that encodes a recombinant protein nonnative to the bacterium for expression within the bacterium. The nonnative recombinant protein is secreted from within the bacterium to outside of the bacterium. The nonnative recombinant protein can also be a non-natural recombinant protein to the extent that it includes domains or molecules that are used by secretion systems within the bacterium to secrete the nonnative recombinant protein.

In one aspect, provided herein is a method of producing a genetically modified bacterium comprising genetically altering a bacterium having one or more genomic nucleic acids encoding a polypeptide secretion system to include an exogenous nucleic acid encoding a recombinant protein including a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and one or more silk fibroin domains or collagen domains, wherein the exogenous nucleic acid is under operation of a promoter to express the recombinant protein.

In some embodiments, the polypeptide secretion system is a Type VIII secretion system or a HlyA Type 1 secretion system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a Sec system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a twin-arginine translocation (Tat) system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a signal recognition particle (SRP) system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a Sec domain or a Tat domain or a signal recognition particle domain. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a component of a Sec system, a component of a Tat system or a component of a signal recognition particle system.

In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a N22 system.

In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a YebF system.

In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and

wherein a domain for directing the recombinant protein to the outer membrane for secretion is an N22 domain or a YebF domain.

In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more of an amyloid domain, an elastin domain or a collagen domain. In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include a CsgA domain. In some embodiments, the exogenous nucleic acid further encodes one or more curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. In some embodiments, the exogenous nucleic acid further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG.

In some embodiments, the recombinant collagen domain comprises bacterial collagen. In some such embodiments, the recombinant collagen comprises one or more bacterial collagen domains, such as a variable domain (V′) and/or a collagen-like domain (CL). In some embodiments, the one or more bacterial collagen domains comprise a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions.

In some embodiments, the bacterium is E. coli. In some embodiments, the bacterium is non-pathogenic.

In some embodiments, the silk fibrin domain includes the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). In some embodiments, the silk fibrin domain includes 4 to 64 repeats of the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3).

In some embodiments, the collagen domain includes the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075). In some embodiments, the collagen domain includes the amino acid sequence

(SEQ ID NO: 2076) GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRG LQGERGEQGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGE AGAQGPAGPMGPAGERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPA GKDGERGPVGPAGKDGQNGQDGLPGKDGKDGQNGKDGLPGKDGKDGQNG KDGLPGKDGKDGQDGKDGLPGKDGKDGLPGKDGKDGQPGKP

In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins. In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins comprising an enzyme, an antibody or a detectable protein.

In one aspect, provided herein is a method for producing one or more silk fibroin domains or one or more collagen domains from a genetically modified bacterium comprising providing the genetically modified bacterium in culture media conditions, wherein the genetically modified bacterium includes one or more genomic nucleic acids encoding a polypeptide secretion system and further including an exogenous nucleic acid encoding a recombinant protein including a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and the one or more silk fibroin domains or collagen domains, wherein the exogenous nucleic acid is under operation of a promoter to express the recombinant protein, and expressing the exogenous nucleic acid to produce the recombinant protein wherein the recombinant protein is secreted from the bacterium and into the surrounding culture media.

In some embodiments, the bacterium is proliferated to produce a population of bacteria cells expressing the exogenous nucleic acid. In some embodiments, the bacterium is proliferated to produce a population of bacteria cells expressing the exogenous nucleic acid to form a biofilm including the recombinant protein.

In some embodiments, the polypeptide secretion system is a Type VIII secretion system or a HlyA Type 1 secretion system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a Sec system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a twin-arginine translocation (Tat) system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a signal recognition particle (SRP) system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a Sec domain or a Tat domain or a signal recognition particle domain. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a component of a Sec system, a component of a Tat system or a component of a signal recognition particle system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a N22 system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a YebF system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein a domain for directing the recombinant protein to the outer membrane for secretion is an N22 domain or a YebF domain.

In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more of an amyloid domain, an elastin domain or a collagen domain. In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include a CsgA domain. In some embodiments, the exogenous nucleic acid further encodes one or more curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. In some embodiments, the exogenous nucleic acid further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG.

In some embodiments, the recombinant collagen domain comprises bacterial collagen. In some such embodiments, the recombinant collagen comprises one or more bacterial collagen domains, such as a variable domain (V′) and/or a collagen-like domain (CL). In some embodiments, the one or more bacterial collagen domains comprise a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions.

In some embodiments, the bacterium is E. coli. In some embodiments, the bacterium is non-pathogenic.

In some embodiments, the silk fibrin domain includes the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). In some embodiments, the silk fibrin domain includes 4 to 64 repeats of the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). In some embodiments, the collagen domain includes the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075). In some embodiments, the collagen domain includes the amino acid sequence GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRGLQGERGE QGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGEAGAQGPAGPMGPA GERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPAGKDGERGPVGPAGKDGQNG QDGLPGKDGKDGQNGKDGLPGKDGKDGQNGKDGLPGKDGKDGQDGKDGLPGKD GKDGLPGKDGKDGQPGKP (SEQ ID NO: 2076) In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins. In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins comprising an enzyme, an antibody or a detectable protein.

In some embodiments, the recombinant protein is unattached to the bacterium. In some embodiments, the recombinant protein is attached to the bacterium.

In another aspect, provided herein is a genetically-modified bacterium comprising one or more genomic nucleic acids encoding a polypeptide secretion system and further including an exogenous nucleic acid encoding a recombinant protein including a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and one or more silk fibroin domains or collagen domains, wherein the exogenous nucleic acid is under operation of a promoter to express the recombinant protein.

In some embodiments, the polypeptide secretion system is a Type VIII secretion system or a HlyA Type 1 secretion system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a Sec system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a twin-arginine translocation (Tat) system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a signal recognition particle (SRP) system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a Sec domain or a Tat domain or a signal recognition particle domain. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a component of a Sec system, a component of a Tat system or a component of a signal recognition particle system. In some embodiments, In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a N22 system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a YebF system. In some embodiments, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein a domain for directing the recombinant protein to the outer membrane for secretion is an N22 domain or a YebF domain.

In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more of an amyloid domain, an elastin domain or a collagen domain. In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include a CsgA domain. In some embodiments, the recombinant collagen domain comprises bacterial collagen. In some such embodiments, the recombinant collagen comprises one or more bacterial collagen domains, such as a variable domain (V′) and/or a collagen-like domain (CL). In some embodiments, the one or more bacterial collagen domains comprise a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions. In some embodiments, the bacterium is E. coli. In some embodiments, the bacterium is non-pathogenic.

In some embodiments, the silk fibrin domain includes the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). In some embodiments, the silk fibrin domain includes 4 to 64 repeats of the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). In some embodiments, the collagen domain includes the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075). In some embodiments, the collagen domain includes the amino acid sequence

(SEQ ID NO: 2076) GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRG LQGERGEQGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGE AGAQGPAGPMGPAGERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPA GKDGERGPVGPAGKDGQNGQDGLPGKDGKDGQNGKDGLPGKDGKDGQNG KDGLPGKDGKDGQDGKDGLPGKDGKDGLPGKDGKDGQPGKP

In some embodiments, the exogenous nucleic acid further encodes one or more curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. In some embodiments, the exogenous nucleic acid further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG.

In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins. In some embodiments, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins comprising an enzyme, an antibody or a detectable protein.

In some embodiments, the recombinant protein is unattached to the bacterium. In some embodiments, the recombinant protein is attached to the bacterium.

In another aspect, provided herein is a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

In yet another aspect, provided herein is a nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

In another aspect, provided herein is a vector comprising a nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

In yet another aspect, provided herein is a bacterium including a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

In another aspect, provided herein is a bacterium including a vector comprising a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

In yet another aspect, provided herein is a bacterium expressing a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin collagen domains.

In another aspect, provided herein is a biofilm including a bacterium expressing a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains. In some embodiments, the silk fibroin domains are spider silk fibrin domains which form spider silk. In some embodiments, the collagen are bacterial collagen domains

In one aspect, provided herein is an engineered bacterium comprising a heterologous nucleic acid encoding a recombinant silk or collagen protein, wherein the recombinant silk or collagen protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, and a silk fibroin domain or one or more collagen domains.

In one embodiment, the recombinant silk protein further comprises an amyloid domain, an elastin domain or a collagen domain. In one embodiment, the recombinant silk protein further comprises an amyloid domain. In one embodiment, the amyloid domain comprises CsgA. In some embodiments, the recombinant collagen domain comprises bacterial collagen. In some such embodiments, the recombinant collagen comprises one or more bacterial collagen domains, such as a variable domain (V′) and/or a collagen-like domain (CL). In some embodiments, the one or more bacterial collagen domains comprise a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains, and may further comprise intervening trypsin-sensitive regions.

In one embodiment, the engineered bacterium comprises a native polypeptide secretion system. In one embodiment, the engineered bacterium further comprises a heterologous nucleic acid encoding a polypeptide secretion system or component of a polypeptide secretion system. In one embodiment, the polypeptide secretion system is a Type VIII secretion system or a HlyA Type 1 secretion system.

In one embodiment, the polypeptide secretion system mediates the transport of a polypeptide from the cytoplasm to the periplasm of the bacterium. In one embodiment, the polypeptide secretion system mediates the secretion of a polypeptide through the outer membrane of the bacterium. In one embodiment, the polypeptide secretion system mediates the transport of a polypeptide from the cytoplasm to the periplasm of the bacterium and through the outer membrane of the bacterium.

In one embodiment, the polypeptide secretion system comprises a Sec system. In one embodiment, the Sec system comprises one or more of SecA, SecB, SecD, SecE, SecF, SecG, SecY, and YajC. In one embodiment, the polypeptide secretion system comprises a twin-arginine translocation (Tat) system. In one embodiment, the Tat system comprises one or more of TatA, TatB, TatE, and TatC. In one embodiment, the polypeptide secretion system is a signal recognition particle (SRP) system. In one embodiment, the SRP system comprises one or more of Ffh, FtsY, and 4.5S RNA.

In one embodiment, the periplasmic translocation signal sequence is a Sec signal sequence, a Tat signal sequence, or a SRP signal sequence. In one embodiment, the periplasmic translocation signal sequence is a Sec signal sequence. In one embodiment, the periplasmic translocation signal sequence is a Tat signal sequence.

In one embodiment, the periplasmic translocation signal sequence is a SRP signal sequence. In one embodiment, the SRP signal sequence comprises the signal sequence of a protein selected from the group consisting of TorT, SfmC, TraU, FocC, TreA, CcmH, FecB, YraI, TolB, AsmA, NikA, FlgI, DsbA, AppA, PcoE, BtuF, PapJ, YbcL, DsbC, ArtJ, ArtI, YraP, YcfS, FlgA, LivK, Agp, ModA, MalE, PhoA, LivJ, FepB, EcoT, MepA, AnsB, and Ivy. In one embodiment, the periplasmic translocation signal sequence comprises an amino acid sequence as set forth in SEQ ID NOs: 10-2029.

In one embodiment, the polypeptide secretion system comprises a curli export system. In one embodiment, the curli export system comprises CsgG. In one embodiment, the curli export system comprises CsgE.

In one embodiment, the polypeptide secretion system comprises a YebF export system. In one embodiment, the YebF export system comprises one or more of OmpC, OmpF and OmpX.

In one embodiment, the outer membrane secretion signal sequence comprises a CsgGE export signal sequence. In one embodiment, the CsgGE export signal sequence comprises the amino acid sequence GVVPQYGGGGNHGGGGNNSGPN (SEQ ID NO: 2030). In one embodiment, the CsgGE export signal sequence comprises an amino acid sequence as set forth in SEQ ID NOs: 2030-2053.

In one embodiment, the outer membrane secretion signal sequence comprises a YebF signal sequence. In one embodiment, the YebF signal sequence comprises the amino acid sequence MKKRGAFLGLLLVSACASVFA (SEQ ID NO: 668).

In one embodiment, the silk fibroin domain comprises a spider silk fibroin domain. In one embodiment, the silk fibroin domain comprises the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). In one embodiment, the recombinant silk protein comprises 1 to 150 repeats of the silk fibroin domain. In one embodiment, the recombinant silk protein comprises 2 to 64 repeats of the silk fibroin domain.

In some embodiments, the collagen domain comprises one or more bacterial collagen domains. In some such embodiments, the collagen domain comprises one or more V′ domains comprising the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075) and/or one or more CL domains comprising the amino acid sequence GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRGLQGERGE QGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGEAGAQGPAGPMGPA GERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPAGKDGERGPVGPAGKDGQNG QDGLPGKDGKDGQNGKDGLPGKDGKDGQNGKDGLPGKDGKDGQDGKDGLPGKD GKDGLPGKDGKDGQPGKP (SEQ ID NO: 2076). In some embodiments, the collagen domain comprises a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions.

In one embodiment, the recombinant silk or collagen protein comprises a functional protein. In one embodiment, the functional protein is selected from the group consisting of an enzyme, an antibody or a detectable protein. In one embodiment, the detectable protein is selected from the group consisting of a poly-histidine tag, a myc tag, a FLAG tag, a hemagglutinin (HA) tag, and a V5 tag.

In one embodiment, the periplasmic translocation signal sequence and the outer membrane secretion signal sequence are located N-terminal to the silk fibroin or collagen domain.

In one embodiment, the heterologous nucleic acid encoding the recombinant silk or collagen protein is operably-linked to a promoter. In one embodiment, the promoter is a constitutive promoter. In one embodiment, the promoter is an inducible promoter.

In one embodiment, the bacterium is E. coli. In one embodiment, the bacterium is non-pathogenic.

In one embodiment, the heterologous nucleic acid encoding the recombinant silk or collagen protein is located in the bacterial chromosome. In one embodiment, the heterologous nucleic acid encoding the recombinant silk or collagen protein is located in a plasmid.

In one aspect, provided herein is a biofilm comprising an engineered bacterium described herein.

In another aspect, provided herein is a method for producing a recombinant silk or collagen protein comprising culturing the engineered bacterium described herein under conditions suitable for the expression of the recombinant silk or collagen protein in the engineered bacterium.

In one embodiment, the recombinant silk or collagen protein is secreted from the engineered bacterium. In one embodiment, the recombinant silk or collagen protein forms curli fibers.

In one embodiment, the methods provided herein further comprise collecting the recombinant silk or collagen protein from the cell culture medium comprising the engineered bacterium. In one embodiment, the methods provided herein further comprise isolating and/or purifying the recombinant silk or collagen protein. In some such embodiments, isolating and/or purifying the recombinant silk or collagen protein comprises affinity chromatography (e.g, nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography), size-based separation via crossflow filtration, and/or acid precipitation.

In another aspect, provided herein is a recombinant silk or collagen polypeptide produced using any one of the methods described herein.

In yet another aspect, provided herein is a curli fiber formed from a plurality of recombinant silk or collagen proteins, wherein the recombinant protein comprises a silk fibroin or bacterial collagen domain and an amyloid domain. In one embodiment, the amyloid domain comprises CsgA.

In one embodiment, the recombinant silk protein comprises a spider silk fibroin domain. In one embodiment, the silk fibroin domain comprises the amino acid sequence of SEQ ID NO: 3. In one embodiment, the recombinant silk protein comprises 1 to 150 repeats of the silk fibroin domain. In one embodiment, the recombinant silk protein comprises 2 to 64 repeats of the silk fibroin domain.

In one embodiment, the recombinant silk protein comprises an elastin domain or a collagen domain.

In some embodiments, the recombinant collagen domain comprises bacterial collagen. In some such embodiments, the recombinant collagen comprises one or more bacterial collagen domains, such as a variable domain (V′) and/or a collagen-like domain (CL). In some embodiments, the one or more bacterial collagen domains comprise a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains, and may further comprise intervening trypsin-sensitive regions.

In one embodiment, the recombinant silk or collagen protein comprises a functional protein. In one embodiment, the functional protein is selected from the group consisting of an enzyme, an antibody or a detectable protein. In one embodiment, the detectable protein is selected from the group consisting of a poly-histidine tag, a myc tag, a FLAG tag, a hemagglutinin (HA) tag, and a V5 tag.

In one aspect, provided herein is a biofilm comprising a curli fiber described herein.

In one aspect, provided herein is a biofilm comprising the collagen proteins described herein. In one aspect, provided herein is a hydrogel comprising the collagen proteins described herein. In one aspect, provided herein is a biomimetic triple-helical fiber meshwork comprising the collagen proteins described herein. In some embodiments, the biofilms and hydrogels disclosed herein comprise a biomimetic triple-helical fiber meshwork comprising the collagen proteins described herein. In some such embodiments, the collagen structures disclosed herein may include physical or chemical modification of the collagen to improve stability, such as by physical or chemical modification. Such crosslinkers are known in the art and include genipen and the like.

In another aspect, provided herein is a nucleic acid encoding a recombinant silk or collagen protein, wherein the recombinant silk or collagen protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, and a silk fibroin or collagen domain.

In one embodiment, the recombinant silk protein further comprises an amyloid domain, an elastin domain or a collagen domain.

In some embodiments, the recombinant collagen domain comprises bacterial collagen. In some such embodiments, the recombinant collagen comprises one or more bacterial collagen domains, such as a variable domain (V′) and/or a collagen-like domain (CL). In some embodiments, the one or more bacterial collagen domains comprise a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains.

In one embodiment, the recombinant silk or collagen protein further comprises an amyloid domain. In one embodiment, the amyloid domain comprises CsgA.

In one embodiment, the periplasmic translocation signal sequence is a Sec signal sequence, a Tat signal sequence, or a SRP signal sequence. In one embodiment, the periplasmic translocation signal sequence is a Sec signal sequence. In one embodiment, the periplasmic translocation signal sequence is a Tat signal sequence.

In one embodiment, the periplasmic translocation signal sequence is a SRP signal sequence. In one embodiment, the SRP signal sequence comprises the signal sequence of a protein selected from the group consisting of TorT, SfmC, TraU, FocC, TreA, CcmH, FecB, YraI, TolB, AsmA, NikA, FlgI, DsbA, AppA, PcoE, BtuF, PapJ, YbcL, DsbC, ArtJ, ArtI, YraP, YcfS, FlgA, LivK, Agp, ModA, MalE, PhoA, LivJ, FepB, EcoT, MepA, AnsB, and Ivy.

In one embodiment, the periplasmic translocation signal sequence comprises an amino acid sequence as set forth in SEQ ID NOs: 10-2029.

In one embodiment, the outer membrane secretion signal sequence comprises a CsgGE export signal sequence. In one embodiment, the CsgGE export signal sequence comprises the amino acid sequence GVVPQYGGGGNHGGGGNNSGPN (SEQ ID NO: 2030). In one embodiment, the CsgGE export signal sequence comprises an amino acid sequence as set forth in SEQ ID NOs: 2030-2053.

In one embodiment, the outer membrane secretion signal sequence comprises a YebF signal sequence. In one embodiment, the YebF signal sequence comprises the amino acid sequence MKKRGAFLGLLLVSACASVFA (SEQ ID NO: 668).

In one embodiment, the silk fibroin domain comprises a spider silk fibroin domain. In one embodiment, the silk fibroin domain comprises the sequence of SEQ ID NO: 3.

In one embodiment, the recombinant silk protein comprises 1 to 150 repeats of the silk fibroin domain. In one embodiment, the recombinant silk protein comprises 2 to 64 repeats of the silk fibroin domain.

In some embodiments, the collagen domain comprises one or more bacterial collagen domains. In some such embodiments, the collagen domain comprises one or more V′ domains comprising the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075) and/or one or more CL domains comprising the amino acid sequence GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRGLQGERGE QGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGEAGAQGPAGPMGPA GERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPAGKDGERGPVGPAGKDGQNG QDGLPGKDGKDGQNGKDGLPGKDGKDGQNGKDGLPGKDGKDGQDGKDGLPGKD GKDGLPGKDGKDGQPGKP (SEQ ID NO: 2076). In some embodiments, the collagen domain comprises a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions.

In one embodiment, the recombinant silk or collagen protein comprises a functional protein. In one embodiment, the functional protein is selected from the group consisting of an enzyme, an antibody or a detectable protein. In one embodiment, the detectable protein is selected from the group consisting of a poly-histidine tag, a myc tag, a FLAG tag, a hemagglutinin (HA) tag, and a V5 tag.

In one embodiment, the periplasmic translocation signal sequence and the outer membrane secretion signal sequence are located N-terminal to the silk fibroin or collagen domain.

In one aspect, provided herein is a vector comprising a nucleic acid described herein. In one embodiment, the nucleic acid is operably-linked to a promoter. In one embodiment, the promoter is a constitutive promoter. In one embodiment, the promoter is an inducible promoter.

Further features and advantages of certain embodiments of the present invention will become more fully apparent in the following description of embodiments and drawings thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing and other features and advantages of the present embodiments will be more fully understood from the following detailed description of illustrative embodiments taken in conjunction with the accompanying drawings in which:

FIG. 1 schematically depicts biomaterials which may be secreted from bacteria according to methods described herein, various fabrication forms and uses.

FIG. 2 depicts in schematic secretion of silk product using the T8SS bacterial functional amyloid secretion system.

FIG. 3A and FIG. 3B schematically depict Sec-N22 secretion tag silk constructs and Sec-N22 amyloid-silk fusion constructs. The silk domain is a repetitive sequence constructed from the Golden Silk Orb-weaving spider Nephila clavipes,

(SEQ ID NO: 3) GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS.

FIG. 4 illustrates that Sec-N22-[Silk]_(N)-HisTag constructs are secreted by the E. coli T8SS pathway. SS-Silk constructs transformed into E. coli and plated onto Congo Red LB plates and induced with 0.05 mM IPTG. The negative control plasmid encodes for a non-CR binding protein, BSA.

FIG. 5 illustrates that Sec-N22-CsgA-[Silk]_(N)-HisTag constructs are secreted by the E. coli T8SS pathway. SS-Silk constructs transformed into E. coli and plated onto Congo Red LB plates and induced with 0.05 mM IPTG. The negative control plasmid encodes for a non-CR binding protein, BSA.

FIG. 6A-6C are schematics showing constructs described herein. FIG. 6A depicts a schematic of an exemplary spider silk only construct. FIG. 6B depicts a schematic of an exemplary CsgA-spider silk fusion construct. FIG. 6C depicts the concatenation cloning scheme.

FIG. 7 schematically represents domain arrangements of potential domain arrangements of recombinant silk proteins described herein.

FIGS. 8A-8E depict extracellular secretion of bacterial collagen from E. coli cells. FIG. 8A depicts the arrangement of the encoding genes of the necessary components for extracellular secretion of the bacterial collagen (bottom) and the existing extracellular secretion pathway for curli fibers consists of SEC, N22, CsgB, CsgA, CsgC, CsgE, CsgF, and CsgG (top, left), and adapted pathway for the secretion of collagen, where CsgB and CsgA are removed (top, right). CsgE and CsgG are necessary in both pathways, while CsgA, CsgB, CsgC and CsgF are only necessary when secreting curli fibers. FIG. 8B depicts distribution of collagen in the bacterial culture after separation of the pellet and supernatant. Detection of his-tagged collagen in each fraction via Western Blot (right) and its representative stained SDS-PAGE gel (left). 1: bacterial culture, 2: supernatant, 3: pellet. FIG. 8C shows scanning electron microscope (SEM) images of bacterial cultures expressing collagen, showing extracellular fibrillar structures. FIGS. 8D and 8E show images of secreted triple helical structures from collagen-secreting PQN4 cells. Images of Sirius Red stained cultures are taken both under light microscope (D) and polarized light microscope (E). The triple helical structure of the collagen appears red under the polarized light, compared with the untransformed PQN4 cells, indicating the collagen secreted extracellularly was able to form stable triple helix. Scale bars: 20 um.

FIG. 9 depicts staining of the supernatant of a culture expressing collagen (A) with Masson's trichrome dye compared with staining of untransformed PQN4 cells (B). Scale bars: 20 um.

FIG. 10 depicts the purification of extracellular collagen using scalable methods. FIG. 10A illustrates the scheme of two scalable purification methods: digestion/precipitation (D-P, top) and digestion/crossflow filtration (D-CF, bottom). Briefly, after the filtration, the collagen domain (CL) is trapped in the retentate and the digested variable domain (V′) and other small digested proteins are removed through permeate. The supernatant is first separated from bacterial cells via centrifugation and digested with pepsin. It is then subjected to separation via precipitation or filtration. In FIG. 10B SDS-PAGE analysis of the purified collagen samples showed comparable purity with collagen/Ni and no fragmentation during the purification; supernatant of the bacterial culture expressed in PQN4 and BL21d (1 and 2), pepsin digested supernatant (3) CL/D-P (4), V′CL/Ni (5), CL/D-CF (6), CL/D-CF (washed with 30 kDa centrifugal filters to remove the remaining impurities) (g). FIG. 10C-10F depicts morphology of the purified proteins observed by SEM; (C) Purified collagen by chromatography (V′CL/Ni) showing the nano/micro-sized fibers, (D) CL/D-CF kept its integrity and fibrillar structure after purification, (E) The aggregated structure of the collagen obtained from D-P method, (F) the collagen obtained from D-P method and protected by erythritol, showing an intact fibrillar structure comparable with V′CL/Ni.

FIG. 11 depicts the optimization of the Ni-NTA purification using 10 mM and 40 mM imidazole solutions for the washing the non-specifically bound proteins and 500 mM imidazole for the elution step. The numbers stand for the number of the collected fractions.

FIGS. 12A-12G depict the structure and triple-helix formation of bacterial collagen. FIG. 12A illustrates the scheme showing the collagen domain containing many charged residues such as E-R and K-D at the N- and C-terminal ends, respectively. FIG. 12B depicts schemes showing the blunt-end (top) and sticky-end (bottom) arrangement of the collagen molecules as a result of interactions between the charged amino acid. FIG. 12C shows the individual extended collagen fibers observed with AFM. One side of the square is 400 nm long. FIG. 12D shows binding of both purified collagen (V′CL/Ni) and type I animal collagen with Sirius-Red. Appearance of the red elongated fibers under the polarized light is an indication of the triple helix formation (Scale bars: 20 um). FIG. 12E CD spectra of the bacterial collagen purified with different methods. After purification with scalable methods, collagen was able to retain its characteristic secondary structure. FIG. 12F shows the effect of pH on the stability of the collagen domain. The low pH decreased the ellipticity value at 220 nm. FIG. 12G shows Raman spectra of the purified collagen samples compared with type I animal collagen. The main spectral biomarkers of the collagen type I are identified, including amide I, amide III, and proline ring.

FIGS. 13A-13C depict bacterial collagen processed under different forms. FIG. 13A shows dried collagen samples after purification with different methods. Lyophilized proteins (top), free-standing thin collagen films (bottom). Scale bars are 1 cm. FIG. 13B shows purified collagen samples cross-linked with genipin with two concentrations (2.5 mM and 5 mM) having absorbance at 600 nm, while FIG. 13C shows that excitation with 590 nm light results in an emission maximum at around 640 nm.

DETAILED DESCRIPTION

In order that the disclosure may be more readily understood, certain terms are first defined. These definitions should be read in light of the remainder of the disclosure and as understood by a person of ordinary skill in the art. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art. Additional definitions are set forth throughout the detailed description.

As used herein, the term “engineered bacterium” or “engineered bacterial cell” refers to a bacterial cell that has been genetically modified from its native state. For instance, an engineered bacterial cell may have nucleotide insertions, nucleotide deletions, nucleotide rearrangements, and nucleotide modifications introduced into their DNA. These genetic modifications may be present in the chromosome of the bacteria or bacterial cell, or on a plasmid in the bacteria or bacterial cell. Engineered bacterial cells of the disclosure may comprise exogenous nucleotide sequences on plasmids. Alternatively, recombinant bacterial cells may comprise exogenous nucleotide sequences stably incorporated into their chromosome. In some embodiments, the engineered bacterium is non-pathogenic. In some embodiments, the engineered bacterium is pathogenic.

As used herein, the term “gene” refers to a nucleic acid fragment that encodes a protein or fragment thereof, optionally including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. In one embodiment, a “gene” does not include regulatory sequences preceding and following the coding sequence.

As used herein, a “heterologous” gene, “heterologous sequence”, or “heterologous nucleic acid” refers to a nucleic acid sequence that is not normally found in a given cell in nature. As used herein, a heterologous sequence encompasses a nucleic acid sequence that is exogenously introduced into a given cell. “Heterologous gene” includes a native gene, or fragment thereof, that has been introduced into the host cell in a form that is different from the corresponding native gene. A heterologous gene may include a native gene, or fragment thereof, introduced into a non-native host cell. Thus, a heterologous gene may be foreign or native to the recipient cell; a nucleic acid sequence that is naturally found in a given cell but expresses an unnatural amount of the nucleic acid and/or the polypeptide which it encodes; and/or two or more nucleic acid sequences that are not found in the same relationship to each other in nature.

As used herein, a “periplasmic translocation signal sequence”, refers to a polypeptide sequence which, when present on a polypeptide, e.g., at the N-terminus of a polypeptide, can cause the polypeptide to be exported from the cytoplasm of a bacterium across the inner membrane. In some embodiments, the periplasmic translocation signal sequence facilitates transport (e.g., export) to the bacterial periplasm as mediated by a bacterial Sec system. In some embodiments, the periplasmic translocation signal sequence facilitates transport (e.g., export) to the bacterial periplasm as mediated by a bacterial twin-arginine translocation (Tat) system. In some embodiments, the periplasmic translocation signal sequence facilitates transport (e.g., export) to the bacterial periplasm as mediated by a bacterial signal recognition particle (SRP) system. In some embodiments, the periplasmic translocation signal sequence is a Sec signal sequence, a Tat signal sequence or a SRP signal sequence and homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the Sec signal sequence comprises a polypeptide having the sequence of E. coli CsgA SecA-dependent secretion signal and homologs and/or variants, including conservative substitution variants, thereof. Periplasmic translocation signal sequences include, but are not limited to, SEQ ID NOs: 10-2029, as disclosed herein. In some embodiments, the periplasmic translocation signal sequence comprises an amino acid sequence having at least 80% homology (e.g., 80% or greater homology, 90% or greater homology, or 95% or greater homology), to the amino acid sequence of a periplasmic translocation signal sequence provided herein e.g. naturally occurring mutations or variants, homologs, or engineered mutations or variants. In some embodiments, the periplasmic translocation signal sequence comprises an amino acid sequence having at least 80%, 81%, 82%, 83% 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of a periplasmic translocation signal sequence provided herein.

As used herein, a “signal recognition particle (SRP) pathway signal sequence” or “SRP signal sequence” refers to a polypeptide sequence which, when present on a polypeptide (e.g., the N-terminus of a polypeptide), can mediate the polypeptide export from the cytoplasm of a bacterium to the periplasmic inner membrane as mediated by the single recognition particle (SRP) pathway proteins. In some embodiments, the polypeptide is translated and transported across the inner membrane concurrently, thus guiding the nascent polypeptide into the periplasm. In some embodiments, the SRP pathway signal sequence is the SRP signal sequence from TorT, SfmC, TraU, FocC, TreA, CcmH, FecB, YraI, TolB, AsmA, NikA, FlgI, DsbA, AppA, PcoE, BtuF, PapJ, YbcL, DsbC, ArtJ, ArtI, YraP, YcfS, FlgA, LivK, Agp, ModA, MalE, PhoA, LivJ, FepB, EcoT, MepA, AnsB, and Ivy, or homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the SRP signal sequence comprises an amino acid sequence having at least 80% homology (e.g., 80% or greater homology, 90% or greater homology, or 95% or greater homology), to the amino acid sequence of a SRP signal sequence provided herein e.g. naturally occurring mutations or variants, homologs, or engineered mutations or variants. In some embodiments, the SRP signal sequence comprises an amino acid sequence having at least 80%, 81%, 82%, 83% 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of a SRP signal sequence provided herein.

As used herein, an “outer membrane secretion signal sequence” refers to a polypeptide sequence which, when present on a polypeptide can cause the polypeptide to be transported across the outer membrane of a bacterial cell (e.g., a Gram-negative bacterial cell). In some embodiments, the outer membrane secretion signal sequence is a CsgGE export signal sequence. In some embodiments, the outer membrane secretion signal sequence is a YebF signal sequence. In some embodiments, the outer membrane secretion signal sequence comprises an amino acid sequence as set forth in the sequence listing. In some embodiments, the outer membrane secretion signal sequence comprises an amino acid sequence having at least 80% homology (e.g., 80% or greater homology, 90% or greater homology, or 95% or greater homology), to the amino acid sequence of an outer membrane secretion signal sequence provided herein e.g. naturally occurring mutations or variants, homologs, or engineered mutations or variants. In some embodiments, the outer membrane secretion signal sequence comprises an amino acid sequence having at least 80%, 81%, 82%, 83% 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of an outer membrane secretion signal sequence provided herein.

As used herein, a “CsgGE export signal sequence” refers to a polypeptide sequence which, when present on a polypeptide can cause the polypeptide to be targeted by CsgE and exported across the outer membrane of the cell via the CsgG oligomeric transport complex of a curli export system, or by an orthologous export system. In some embodiments, the CsgGE export signal sequence comprises the last 22 amino acids of the bipartite curli signal sequence of an endogenous polypeptide exported by the curli export system. In some embodiments, the CsgGE export signal sequence comprises be a polypeptide having the sequence of an E. coli CsgA CsgGE export signal sequence (e.g., GVVPQYGGGGNHGGGGNNSGPN; SEQ ID NO: 2030; also referred to herein as N22 domain) and homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the CsgGE export signal sequence comprises an amino acid sequence as set forth in SEQ ID NOs: 2030-2053. In some embodiments, the CsgGE export signal sequence comprises an amino acid sequence having at least 80% homology (e.g., 80% or greater homology, 90% or greater homology, or 95% or greater homology), to the amino acid sequence of a CsgGE export signal sequence provided herein e.g. naturally occurring mutations or variants, homologs, or engineered mutations or variants. In some embodiments, the CsgGE export signal sequence comprise an amino acid sequence having at least 80%, 81%, 82%, 83% 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of a CsgGE export signal sequence provided herein.

A “polypeptide secretion system”, as used herein, refers to one or more proteins, nucleic acids, and/or cofactors that mediate the export of a polypeptide from the cytoplasm of a bacterial cell (e.g., through the inner membrane, to the periplasm, through the outer membrane, to the cell surface and/or to the extracellular milieu of a bacterial cell). In some embodiments, the bacterial cell is a Gram-negative bacterial cell. In some embodiments, the bacterial cell is a Gram-positive bacterial cell.

A “promoter” as used herein, refers to a nucleotide sequence that is capable of controlling the expression of a coding sequence or gene. Promoters are generally located 5′ of the sequence that they regulate. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from promoters found in nature, and/or comprise synthetic nucleotide segments. Those skilled in the art will readily ascertain that different promoters may regulate expression of a coding sequence or gene in response to a particular stimulus, e.g., in a cell-specific or tissue-specific manner, in response to different environmental or physiological conditions, or in response to specific compounds. Prokaryotic promoters are typically classified into two classes: inducible and constitutive.

“Constitutive promoter” refers to a promoter that is capable of facilitating continuous transcription of a coding sequence or gene under its control and/or to which it is operably linked. Constitutive promoters and variants are well known in the art and include, but are not limited to, a constitutive Escherichia coli GS promoter, a constitutive Escherichia coli G32 promoter, a constitutive Escherichia coli G70 promoter, a constitutive Bacillus subtilis GA promoter, a constitutive Bacillus subtilis GB promoter, and a bacteriophage T7 promoter.

An “inducible promoter” refers to a promoter that initiates increased levels of transcription of the coding sequence or gene under its control in response to a stimulus or an exogenous environmental condition. A “directly inducible promoter” refers to a regulatory region, wherein the regulatory region is operably linked to a gene encoding a protein or polypeptide, where, in the presence of an inducer of said regulatory region, the protein or polypeptide is expressed. An “indirectly inducible promoter” refers to a regulatory system comprising two or more regulatory regions, for example, a first regulatory region that is operably linked to a first gene encoding a first protein, polypeptide, or factor, e.g., a transcriptional regulator, which is capable of regulating a second regulatory region that is operably linked to a second gene, the second regulatory region may be activated or repressed, thereby activating or repressing expression of the second gene. Both a directly inducible promoter and an indirectly inducible promoter are encompassed by “inducible promoter.” As used herein, the term “expression” refers to the transcription and stable accumulation of sense (mRNA) or anti-sense RNA derived from a nucleic acid, and/or to translation of an mRNA into a polypeptide

The term “genetic modification,” as used herein, refers to any genetic change. Exemplary genetic modifications include those that increase, decrease, or abolish the expression of a gene, including, for example, modifications of native chromosomal or extrachromosomal genetic material. Exemplary genetic modifications also include the introduction of at least one plasmid, modification, mutation, base deletion, base addition, and/or codon modification of chromosomal or extrachromosomal genetic sequence(s), gene over-expression, gene amplification, gene suppression, promoter modification or substitution, gene addition (either single or multi-copy), antisense expression or suppression, or any other change to the genetic elements of a host cell, whether the change produces a change in phenotype or not. Genetic modification can include the introduction of a plasmid, e.g., a plasmid comprising at least one amino acid catabolism enzyme operably linked to a promoter, into a bacterial cell. Genetic modification can also involve a targeted replacement in the chromosome, e.g., to replace a native gene promoter with an inducible promoter, regulated promoter, strong promoter, or constitutive promoter. Genetic modification can also involve gene amplification, e.g., introduction of at least one additional copy of a native gene into the chromosome of the cell. Alternatively, chromosomal genetic modification can involve a genetic mutation.

The term “isolated” or “partially purified” as used herein refers, in the case of a nucleic acid or polypeptide, to a nucleic acid or polypeptide separated from at least one other component (e.g., nucleic acid or polypeptide) that is present with the nucleic acid or polypeptide as found in its natural source and/or that would be present with the nucleic acid or polypeptide when expressed by a cell, or secreted in the case of secreted polypeptides. A chemically synthesized nucleic acid or polypeptide or one synthesized using in vitro transcription/translation is considered “isolated.”

As used herein, the term “exogenous” refers to a substance (e.g., a nucleic acid or polypeptide) present in a cell other than its native source. The term exogenous can refer to a nucleic acid or a protein that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is not normally found or in which it is found in undetectable amounts. A substance can be considered exogenous if it is introduced into a cell or an ancestor of the cell that inherits the substance. In contrast, the term “endogenous” or “native” refers to a substance that is naturally-present in the biological system or cell.

A “plasmid” or “vector” includes a nucleic acid construct designed for delivery to a host cell or transfer between different host cell. An “expression plasmid” or “expression vector” can be a plasmid that has the ability to incorporate and express heterologous nucleic acid fragments in a cell. An expression plasmid may comprise additional elements, for example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms. The nucleic acid incorporated into the plasmid can be operatively linked to an expression control sequence when the expression control sequence controls and regulates the transcription and translation of that polynucleotide sequence.

As used herein, the terms “protein” and “polypeptide” are used interchangeably herein to designate a series of amino acid residues, connected to each other by peptide bonds between the alpha-amino and carboxy groups of adjacent residues. The terms “protein”, and “polypeptide” refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogs, regardless of its size or function. The terms “protein” and “polypeptide” as used herein refer to both large polypeptides and small peptides. The terms “protein” and “polypeptide” are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogs of the foregoing.

The term “operatively linked” includes having an appropriate transcription start signal (e.g., promoter) in front of the polynucleotide sequence to be expressed, and having an appropriate translation start signal (e.g., a Shine Delgarno sequence and a start codon (ATG)) in front of the polypeptide coding sequence and maintaining the correct reading frame to permit expression of the polynucleotide sequence under the control of the expression control sequence, and, optionally, production of the desired polypeptide encoded by the polynucleotide sequence. In some examples, transcription of a gene encoding a recombinant polypeptide as described herein is under the control of a promoter sequence (or other transcriptional regulatory sequence) which controls the expression of the nucleic acid in a cell-type in which expression is intended. It will also be understood that the gene encoding a recombinant polypeptide as described herein can be under the control of transcriptional regulatory sequences which are the same or which are different from those sequences which control transcription of the naturally-occurring form of a protein.

The terms “overexpression” or “overexpress”, as used herein refers to the expression of a functional nucleic acid, polypeptide or protein encoded by DNA in a host cell, wherein the nucleic acid, polypeptide or protein is either not normally present in the host cell, or wherein the nucleic acid, polypeptide or protein is present in the host cell at a higher level than that normally expressed from the endogenous gene encoding the nucleic acid, polypeptide or protein.

A “nucleic acid” or “nucleic acid sequence” may be any molecule, preferably a polymeric molecule, incorporating units of ribonucleic acid, deoxyribonucleic acid or an analog thereof. The nucleic acid can be either single-stranded or double-stranded. A single-stranded nucleic acid can be one nucleic acid strand of a denatured double-stranded DNA. Alternatively, it can be a single-stranded nucleic acid not derived from any double-stranded DNA. In one aspect, the nucleic acid can be DNA. In another aspect, the nucleic acid can be RNA. Suitable nucleic acid molecules are DNA, including genomic DNA or cDNA. Other suitable nucleic acid molecules are RNA, including mRNA.

The term “non-pathogenic” as used herein to refer to bacteria refers to bacteria that are not capable of causing disease or harmful responses in a host. In some embodiments, non-pathogenic bacteria are commensal bacteria. Naturally pathogenic bacteria may be genetically engineered to provide reduce or eliminate pathogenicity.

With respect to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid and retains the desired activity of the polypeptide. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles consistent with the disclosure. A given amino acid can be replaced by a residue having similar physiochemical characteristics, e.g., substituting one aliphatic residue for another (such as Ile, Val, Leu, or Ala for one another), or substitution of one polar residue for another (such as between Lys and Arg; Glu and Asp; or Gln and Asn). Other such conservative substitutions, e.g., substitutions of entire regions having similar hydrophobicity characteristics, are well known. Polypeptides comprising conservative amino acid substitutions can be tested in any one of the assays described herein to confirm that a desired activity. Amino acids can be grouped according to similarities in the properties of their side chains (in A. L. Lehninger, in Biochemistry, second ed., pp. 73-75, Worth Publishers, New York (1975)): (1) non-polar: Ala (A), Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W), Met (M); (2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gln (Q); (3) acidic: Asp (D), Glu (E); (4) basic: Lys (K), Arg (R), His (H). Alternatively, naturally occurring residues can be divided into groups based on common side-chain properties: (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Be; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; (6) aromatic: Trp, Tyr, Phe. Non-conservative substitutions will entail exchanging a member of one of these classes for another class. Particular conservative substitutions include, for example; Ala into Gly or into Ser; Arg into Lys; Asn into Gln or into His; Asp into Glu; Cys into Ser; Gln into Asn; Glu into Asp; Gly into Ala or into Pro; His into Asn or into Gln; Be into Leu or into Val; Leu into Ile or into Val; Lys into Arg, into Gln or into Glu; Met into Leu, into Tyr or into Be; Phe into Met, into Leu or into Tyr; Ser into Thr; Thr into Ser; Trp into Tyr; Tyr into Trp; and/or Phe into Val, into Be or into Leu.

In some embodiments, polypeptide described herein can be a variant of a sequence described herein, e.g., a conservative substitution variant of a polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments, the variant is a conservatively modified variant. Conservative substitution variants can be obtained by mutations of native nucleotide sequences, for example. A “variant,” as referred to herein, is a polypeptide substantially homologous to a native or reference polypeptide, but which has an amino acid sequence different from that of the native or reference polypeptide because of one or a plurality of deletions, insertions or substitutions. Variant polypeptide-encoding DNA sequences encompass sequences that comprise one or more additions, deletions, or substitutions of nucleotides when compared to a native or reference DNA sequence, but that encode a variant protein or fragment thereof that retains activity, e.g. ability to target a polypeptide for export via the curli export system. A wide variety of PCR-based site-specific mutagenesis approaches are also known in the art and can be applied by the ordinarily skilled artisan.

A variant amino acid or DNA sequence can be at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more, identical to a native or reference sequence. The degree of homology (percent identity) between a native and a mutant sequence can be determined, for example, by comparing the two sequences using freely available computer programs commonly employed for this purpose on the world wide web (e.g., BLASTp or BLASTn with default settings).

Alterations of the native amino acid sequence can be accomplished by any of a number of techniques known to one of skill in the art. Mutations can be introduced, for example, at particular loci by synthesizing oligonucleotides containing a mutant sequence, flanked by restriction sites enabling ligation to fragments of the native sequence. Following ligation, the resulting reconstructed sequence encodes an analog having the desired amino acid insertion, substitution, or deletion. Alternatively, oligonucleotide-directed site-specific mutagenesis procedures can be employed to provide an altered nucleotide sequence having particular codons altered according to the substitution, deletion, or insertion required. Techniques for making such alterations are very well established and include, for example, those disclosed by Walder et al. (Gene 42:133, 1986); Bauer et al. (Gene 37:73, 1985); Craik (BioTechniques, January 1985, 12-19); Smith et al. (Genetic Engineering: Principles and Methods, Plenum Press, 1981); and U.S. Pat. Nos. 4,518,584 and 4,737,462, which are herein incorporated by reference in their entireties. Any cysteine residue not involved in maintaining the proper conformation of the polypeptide also can be substituted, generally with serine, to improve the oxidative stability of the molecule and prevent aberrant crosslinking. Conversely, cysteine bond(s) can be added to the polypeptide to improve its stability or facilitate oligomerization.

Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages can mean±1%.

The articles “a” and “an,” as used herein, should be understood to mean “at least one,” unless clearly indicated to the contrary.

The phrase “and/or,” when used between elements in a list, is intended to mean either (1) that only a single listed element is present, or (2) that more than one element of the list is present. For example, “A, B, and/or C” indicates that the selection may be A alone; B alone; C alone; A and B; A and C; B and C; or A, B, and C. The phrase “and/or” may be used interchangeably with “at least one of” or “one or more of” the elements in a list.

Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.

In one aspect, the present disclosure is directed to the use of a secretion system in a bacterium to secrete a non-native polypeptide from the bacterium and into the surrounding environment. The bacterium may be genetically-altered to include a heterologous encoding the nonnative polypeptide. In some embodiments, the non-native polypeptide is expressed and secreted from the bacterium using a bacterial secretion system which may be native to the bacterium or non-native to the bacterium. A bacterial secretion system which is nonnative to the bacterium is one which has been introduced into the bacterium, for example, through genetic modification of the bacterium to include nucleic acids encoding the non-native or foreign secretion system or components of a non-native secretion system. In some embodiments, the non-native polypeptide is expressed by the bacterium but not secreted from the bacterium.

In one aspect, the present invention provides an engineered bacterium comprising a heterologous nucleic acid encoding a recombinant silk or collagen protein, wherein the recombinant silk or collagen protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, and a silk fibroin or collagen domain. Without wishing to be bound by any particular theory, the expression of the recombinant silk or collagen proteins comprising said signal sequence provides for the robust production and secretion of said proteins which may be readily purified and used for multiple applications.

In some embodiments, the heterologous nucleic acid encoding a recombinant silk or collagen protein comprises a heterologous nucleic acid encoding a periplasmic translocation signal sequence. In some embodiments, the periplasmic translocation signal sequence facilitates the export of the recombinant silk polypeptide from the cytoplasm of the bacterium to the periplasm of the bacterium via an endogenous or heterologous polypeptide secretion system. In some embodiments, the heterologous nucleic acid encoding a recombinant silk or collagen protein comprises multiple heterologous nucleic acid sequences encoding a periplasmic translocation signal sequence (e.g., one, two, three, four, five, or six nucleic acid sequences encoding a periplasmic translocation signal sequence). In some embodiments, the polypeptide secretion system that mediates the secretion of the polypeptide from the cytoplasm to the periplasmic space of the bacterium is a Sec system, a twin-arginine translocation (Tat) system, or a signal recognition particle (SRP) system. In some embodiments, the heterologous nucleic acid encoding recombinant silk or collagen protein encodes a periplasmic translocation signal sequence selected from the group consisting of a Sec signal sequence, a Tat signal sequence, and a SRP signal sequence. In some embodiments, the recombinant silk or collagen protein comprises a periplasmic translocation signal sequence. In some embodiments, the recombinant silk or collagen protein comprises a periplasmic translocation signal sequence selected from the group consisting of a Sec signal sequence, a Tat signal sequence, and a SRP signal sequence. In some embodiments, the recombinant silk or collagen protein comprises multiple periplasmic translocation signal sequences (e.g., one, two, three, four, five, or six periplasmic translocation signal sequences). In some embodiments, the periplasmic translocation sequence is N-terminal of the polypeptide. In some embodiments, the periplasmic translocation signal sequence is N-terminal of the outer membrane secretion signal sequence. In some embodiments, the periplasmic translocation sequence is C-terminal of the outer membrane secretion signal sequence. Other polypeptide secretion systems that mediate the transport (e.g., export) of polypeptides from the cytoplasm to the periplasmic space of the bacterium and their cognate signal peptides are known in the art and may be used as described herein (see, e.g., Green and Mecsas (2016) Microbiol. Spectr. 4:1; doi: 10.1128/microbiolspec.VMBF-0012-2015, the contents of which are incorporated herein by reference).

Bacterial secretion systems may be used to secrete a silk protein described herein (e.g., a silk protein comprising a silk fibroin domain) or a collagen protein described herein (e.g., bacterial collagen comprising one more V′ and/or CL domains) through a heterologous system evolved for the secretion of other proteins. Such secretions systems are known to those of skill in the art and include, for example: 1) systems for periplasmic secretion, and 2) systems for secretion from the periplasm, across the outer membrane, and into the extracellular milieu. An exemplary system for periplasmic secretion includes a Twin-arginine Translocation (Tat) system which exports fully folded proteins to the periplasm (see, e.g., Lee P A, Tullman-Ercek D, Georgiou G, “The bacterial twin-arginine translocation pathway”, Annu Rev Microbiol. 60:373-95 (2006) PMID: 16756481, which is hereby incorporated by reference in its entirety). An exemplary system for periplasmic secretion includes a Signal Recognition Particle (SRP) system which mediates co-translational secretion into the periplasm (see, e.g., Saraogi I, Shan S O, “Co-translational protein targeting to the bacterial membrane”, Biochim. Biophys. Acta. 1843(8): 1433-41 (2014) doi: 10.1016/j.bbamcr.2013.10.013, PMID: 24513458, which is hereby incorporated by reference in its entirety).

The Sec system, also known as the Sec secretion pathway, primarily translocates proteins to the periplasmic space in their unfolded state (see, e.g., Beckwith (2013) Res. Microbiol. 164(6): 497-504). The Sec system consists of a protein targeting component, a motor protein and a membrane-integrated channel, called the SecYEG translocase complex, which is stably formed by the SecY, SecE and SecG proteins (encoded by the secY, secE and secG genes, respectively). SecB (encoded by the secB gene) is a chaperone protein that interacts with the nascent chain of the proteins preventing their folding. SecA (encoded by the secA gene) is an ATPase that interacts with SecB as well as the SecYEG translocase complex. Proteins not requiring SecB to prevent folding may be recognized by SecA and transferred during synthesis to the SecYEG translocase complex. SecA remains bound to SecYEG translocase complex as the protein is translocated and is released when the export is complete. Additional proteins that may be involved in the Sec system-mediated export of proteins from the cytoplasm to the periplasmic space include SecD and SecF (encoded by the secD and secF genes, respectively), which form the SecDF complex and may function as chaperone proteins, and YajC (encoded by the yajC gene) which co-purifies with the SecDF complex. The function of YajC is unclear.

In some embodiments, the bacterium comprises an endogenous Sec system. In some embodiments, the bacterium comprises an endogenous secY gene. In some embodiments, the bacterium comprises an endogenous secE gene. In some embodiments, the bacterium comprises an endogenous secG gene. In some embodiments, the bacterium comprises an endogenous secB gene. In some embodiments, the bacterium comprises an endogenous secA gene. In some embodiments, the bacterium comprises an endogenous secD gene. In some embodiments, the bacterium comprises an endogenous secF gene. In some embodiments, the bacterium comprises an endogenous yajC gene.

In some embodiments, the bacterium has been genetically-modified to comprise a heterologous Sec system. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous secY gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous secE gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous secG gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous secB gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous secA gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous secD gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous secF gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous yajC gene. In some embodiments, the bacterium has been genetically-modified to comprise one or more of a heterologous secY gene, a heterologous secE gene, a heterologous secG gene, a heterologous secB gene, a heterologous secA gene, a heterologous secD gene, a heterologous secF gene, and a heterologous yajC gene.

The twin arginine Tat system, also known as the Tat pathway, mediates the translocation of folded proteins across lipid bilayers, for example, from the cytoplasm to the periplasmic space (see, e.g., Robinson et al. (2011) Biochimica et Biophysica Acta 1808: 876-884; and Goosens et al. (2014) Biochimica et Biophysica Acta 1843: 1698-1706. Tat systems are present in both Gram-negative and Gram-positive bacteria. In E. coli, the Tat system is comprised of TatA, TatB and TatC subunits which mediate protein translocation, and are encoded by tatA, tatB and tatC genes. In E coli, an additional subunit TatE, encoded by the tatE gene partially complements tatA null mutants and appears to be redundant.

In some embodiments, the bacterium comprises an endogenous Tat system. In some embodiments, the bacterium comprises an endogenous tatA gene. In some embodiments, the bacterium comprises an endogenous tatB gene. In some embodiments, the bacterium comprises an endogenous tatC gene. In some embodiments, the bacterium comprises an endogenous tatE gene. In some embodiments, the bacterium comprises an endogenous tatABC operon.

In some embodiments, the bacterium has been genetically-modified to comprise a heterologous Tat system. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous tatA gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous tatB gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous tatC gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous tatE gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous tatABC operon. In some embodiments, the bacterium has been genetically-modified to comprise one or more of a heterologous tatA gene, a heterologous tatB gene, a heterologous tatC gene, a heterologous tatE gene, and a heterologous tatABC operon.

The SRP pathway is a polypeptide transport system in bacterial cells which mediates the co-translational translocation of proteins through the inner membrane and into the periplasm. In the SRP system, a specific N-terminal protein sequence is recognized by a complex comprising, Ffh protein and a 4.5S RNA, which guides the nascent polypeptide chain directly into the periplasm via the FtsY receptor. In some embodiments, the SRP pathway signal sequence is cleavable (see, e.g., Schierle et al. (2003) J. Bacteriol. 185(19): 5706-13). Any known SRP pathway signal sequences can be used as described herein.

In some embodiments, the bacterium has been genetically-modified to comprise a heterologous ffh gene (which encodes Ffh protein). In some embodiments, the bacterium has been genetically-modified to comprise a heterologous ftsY gene (which encodes the signal recognition particle receptor protein FtsY). In some embodiments, the bacterium has been genetically engineered to comprise a heterologous ffs gene (which encodes 4.5S RNA). In some embodiments, the bacterium has been genetically-modified to comprise one or more of a heterologous ffh gene, a heterologous ftsY gene, and a heterologous ffs gene.

In some embodiments, the recombinant silk or collagen protein comprises a SRP signal sequence. In some embodiments, the heterologous nucleic acid encoding the recombinant silk or collagen protein comprises a SRP signal sequence selected from the group consisting of the SRP signal sequence comprises the signal sequence of a protein selected from the group consisting of TorT, SfmC, TraU, FocC, TreA, CcmH, FecB, YraI, TolB, AsmA, NikA, FlgI, DsbA, AppA, PcoE, BtuF, PapJ, YbcL, DsbC, ArtJ, ArtI, YraP, YcfS, FlgA, LivK, Agp, ModA, MalE, PhoA, LivJ, FepB, EcoT, MepA, AnsB, and Ivy, or homologs and/or variants, including conservative substitution variants, thereof.

In some embodiments, the recombinant silk or collagen protein comprises a periplasmic translocation signal sequence comprising an amino acid sequence as set forth in the sequence listing, or homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the heterologous nucleic acid encoding the recombinant silk or collagen protein comprises a periplasmic translocation signal sequence comprising an amino acid sequence as set forth in the sequence listing, or homologs and/or variants, including conservative substitution variants, thereof.

In some embodiments, the heterologous nucleic acid encoding the recombinant silk or collagen protein comprises a heterologous nucleic acid encoding an outer membrane secretion signal sequence. In some embodiments, the heterologous nucleic acid encoding a recombinant silk or collagen protein comprises multiple heterologous nucleic acid sequences encoding an outer membrane secretion signal sequence (e.g., one, two, three, four, five, or six nucleic acid sequences encoding an outer membrane secretion signal sequence). In some embodiments, the recombinant silk or collagen protein comprises an outer membrane secretion signal sequence. In some embodiments, the recombinant silk or collagen protein comprises multiple outer membrane secretion signal sequences (e.g., one, two, three, four, five, or six outer membrane secretion signal sequence). In some embodiments, the outer membrane secretion signal sequence is N-terminal of the outer membrane secretion signal sequence. In some embodiments, the outer membrane secretion signal sequence is C-terminal of the periplasmic translocation signal sequence. The outer membrane signal sequence mediates the secretion of the protein through the outer membrane of the bacterium.

In some embodiments, the outer membrane signal sequence mediates the transport of the protein via a curli export system. In some embodiments, the outer membrane export signal sequence is a CsgGE export signal sequence, or homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the heterologous nucleic acid encoding the recombinant silk or collagen protein comprises a heterologous nucleic acid encoding a CsgGE export signal sequence, or homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the recombinant silk or collagen protein comprises a CsgGE export signal sequence, or homologs and/or variants, including conservative substitution variants, thereof. The CsgGE export signal sequence facilitates the transport of a polypeptide comprising the CsgGE export signal sequence from the bacterial periplasm via a bacterial type-8 secretion system. The Type-8 Secretion System (T8SS) of Gram-negative bacteria, such as Escherichia coli, is a dedicated protein export system that has evolved for the secretion of functional amyloids (e.g., an amyloid polypeptide) to the extracellular space. These amyloids then self-assemble to form nanofibers implicated in pathogenesis of epithelial tissue and biofilm persistence (Chapman et al. (2002) Science 295(5556): 851-855). The outer membrane porin for the T8SS is composed of nonameric outer membrane protein, CsgG. The fully assembled CsgG complex contains a 2 nm transmembrane channel (Goyal et al. (2014) Nature 516: 250-3). The structural monomeric unit of the functional amyloid, CsgA, is exported to the extracellular space via CsgG through a specific CsgG-specific N-terminal peptide tag, called N22. This event is preceded by translocation of the cytoplasmically-expressed CsgA protein to the periplasm through the Sec system, the major periplasmic export system in bacteria. An additional periplasmically-localized protein, CsgE, confers N22-containing substrate specificity for CsgG export and forms a multimeric complex with CsgG, encapsulating the protein to be exported and creating an entropic free-energy gradient that is thought to drive the export through the CsgG channel. In the absence of CsgE, the CsgG porin is ungated, allowing for passive diffusion of molecules through the outer membrane (Nenninger et al. (2011) Molecular Microbiology 81(2): 486-499).

In some embodiments, the CsgGE export signal sequence is an E. coli CsgGE export signal sequence. In some embodiments, the E. coli CsgGE export signal sequence comprises the amino acid sequence GVVPQYGGGGNHGGGGNNSGPN (SEQ ID NO: 2030; referred to herein as N22).

Any CsgGE export signal sequence known in the art and homologs and/or variants, including conservative substitution variants, may be used as described herein. In some embodiments, the CsgGE export signal sequence comprises an amino acid sequence as set forth in the sequence listing, or homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the CsgGE export signal sequences comprises an amino acid sequence selected from the group consisting of GVVPQYGGGGNHGGGGNNSGPN (SEQ ID NO: 2030), GVVPQWGGGGNHNGGGNSSGPD (SEQ ID NO: 2031), GVVPQYGGGNHGGGNGGGSNNSGPN (SEQ ID NO: 2032), GVVPQYGGGGNHGGGGN (SEQ ID NO: 2033), IPQYGGGNHGGGGNNSGPN (SEQ ID NO: 2034), IPQFGGGGHHGGGGNNSGPN (SEQ ID NO: 2035), GVVPQWGGGGNHNGGGNNSGPD (SEQ ID NO: 2036), IPQYGGGGGNHGGGGNNSGPN (SEQ ID NO: 2037), GAIPQYGGGGGGNHGGGGNNSGPN (SEQ ID NO: 2038), IPQYGGGGNHGGGGNNSGPN (SEQ ID NO: 2039), GVVPQYGGGNHGGGGNNSGPN (SEQ ID NO: 2040), GVVPQYGGGGNLGGGGNNSGPN (SEQ ID NO: 2041), GVVPQYGGGGNYGGGGNNSGPN (SEQ ID NO: 2042), GAVPQFGGGHGGGWGGGNNGPD (SEQ ID NO: 2043), GAIPQYGHGGGWGGGNSGPN (SEQ ID NO: 2044), IPQYGGGHGGGSNNGP (SEQ ID NO: 2045), GAVPQFGGHGHGHGGGGNSGPD (SEQ ID NO: 2046), GLVPQYGGGHGGGNTTGP (SEQ ID NO: 2047), GVVPQWGGNHHGGGNNYGPD (SEQ ID NO: 2048), GVVPQWGGSGHHNGGNNNGPD (SEQ ID NO: 2049), VPQYGNGGGHGGGSNGPN (SEQ ID NO: 2050), GLVPQYGGGHGGGGSTTGP (SEQ ID NO: 2051), VPQYGHGGNGGWGGNNGGPN (SEQ ID NO: 2052), GTVPQFGGGGGHNPGNGNNNGPN (SEQ ID NO: 2053), or homologs and/or variants, including conservative substitution variants, thereof. In addition, any export signal sequence that mediates the export of a polypeptide to the extracellular milieu that is orthologous to a curli export system may be used as described herein.

In some embodiments, the bacterium has been genetically-modified to comprise a heterologous csgE gene (which encodes CsgE). In some embodiments, the heterologous csgE gene is an E. coli csgE gene. In some embodiments, the bacterium has been genetically-engineered to comprise a heterologous csgG gene. In some embodiments, the heterologous csgE gene is an E. coli csgG gene (which encodes CsgG). In some embodiments, the bacterium has been genetically-modified to comprise a heterologous csgE gene and a heterologous csgG gene.

In some embodiments, the outer membrane signal sequence mediates the transport of the protein via a YebF export system. In some embodiments, the heterologous nucleic acid encoding the recombinant silk or collagen protein comprises a heterologous nucleic acid encoding a YebF signal sequence, or homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the recombinant silk or collagen protein comprises a YebF signal sequence, or homologs and/or variants, including conservative substitution variants, thereof. In some embodiments, the YebF signal sequence comprises the amino acid sequence as set forth in the sequence listing, or homologs and/or variants, including conservative substitution variants, thereof. The YebF export system mediates the secretion of a protein of interest by fusion to the YebF protein, which is secreted by E. coli (see, e.g., Zhang et al. (2006) Nat. Biotechnol. 24(1): 100-4; and Prehna et al. (2012) Structure 20(7): 1154-66, the contents of each which are hereby incorporated by reference in their entirety). The outer membrane proteins OmpC, OmpF, and OmpX (encoded by the ompC, ompF and ompX genes, respectively) mediate the outer membrane export of the YebF protein.

In some embodiments, the bacterium has been genetically-modified to comprise a heterologous ompC gene. In some embodiments, the bacterium has been genetically-engineered to comprise a heterologous ompF gene. In some embodiments, the bacterium has been genetically-modified to comprise a heterologous ompX gene. In some embodiments, the bacterium has been genetically-modified to comprise one or more of a heterologous ompC gene, a heterologous ompF gene, and a heterologous ompX gene.

Other exemplary system for secretion through the outer membrane includes the HlyA Type 1 secretion system (T1SS), which mediates secretion from the cytoplasm directly into the extracellular space via the hemolysin export system (see, e.g., Thomas et al., “The Type 1 secretion pathway—the hemolysin system and beyond”, Biochim Biophys Acta 1843(8): 1629-41 (2014), doi:10.1016/j.bbamcr.2013.09.017, PMID:24129268, which is hereby incorporated by reference in its entirety).

In some embodiments, the heterologous nucleic acid encoding the recombinant silk or collagen protein comprises a heterologous nucleic acid encoding a silk fibroin or collagen domain. In some embodiments, the recombinant silk or collagen protein comprises a silk fibroin domain. A nonnative polypeptide within the scope of the present disclosure is spider silk or bacterial collagen. In some embodiments, the silk fibroin domain is a spider silk fibroin domain. Spider silk is composed of two major fibroin proteins, or ‘spidroins’, which are repetitive modular proteins of high molecular weight. The primary structure of the spidroin consists of ordered amino- and carboxy-terminal regions that flank a core domain rich in alanine and glycine residues. After secretion and spinning by the spider, the spider silk matures into a semicrystalline material wherein regions of self-assembled regularly ordered domains are embedded in an amorphous matrix. The ordered domains consist of antiparallel beta-sheet crystals that are encoded by poly-(Gly-Ala) and poly-Ala repeats. Confined hydrogen bonding networks between these crystalline beta-sheets are thought to underpin the unique mechanical properties of silk (see, e.g., Keten, S., Xu, Z., Ihle, B. & Buehler, M. J., “Nanoconfinement controls stiffness, strength and mechanical toughness of β-sheet crystals in silk”, Nat. Mater. 9, 359-367 (2010); and Nova, A., Keten, S., Pugno, N. M., Redaelli, A. & Buehler, M. J., “Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils”, Nano Lett. 10, 2626-34 (2010)).

In some embodiments, the heterologous nucleic acid encoding the recombinant silk protein comprises a heterologous nucleic acid encoding a 1 to 150 repeats of a silk fibroin domain. In some embodiments, the recombinant silk protein comprises a 1 to 150 repeats of a silk fibroin domain. In some embodiments, the heterologous nucleic acid encoding the recombinant silk protein comprises a heterologous nucleic acid encoding a 2 to 64 repeats of a silk fibroin domain. In some embodiments, the recombinant silk protein comprises a 2 to 64 repeats of a silk fibroin domain. In some embodiments, the recombinant silk protein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 61, 63, 64, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 silk fibroin domains. The combination of repeats of silk fibroin domain may comprise silk fibroin domains of the same type or of different types. In some embodiments, the silk fibroin domain is selected from the group consisting of a minor ampullate silk fibroin domain, an aggregate silk fibroin domain, a flagelliform (flag) silk fibroin domain, a tubulin silk fibroin domain, an aciniform silk fibroin domain and a piriform silk fibroin domain. In some embodiments, the silk fibroin domain comprises a consensus amino acid sequence as set forth in the sequence listing (see, e.g., Lewis (2006) Chem. Rev. 106(9): 3762-74, the entire contents of which are incorporated herein be reference). In some embodiments, the silk fibroin domain comprises the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3).

In some embodiments, the silk fibroin domain comprises an amino acid sequence as set forth in NCBI Database Accession Numbers: AAT08436.1, ADM14316.1, ADM14324.1, ADM14315.1, ADM14325.1, OEH77770.1, GAP79055.1, AKJ27708.1, ABD66603.1, ABD66602.1, CAM32263.1, CAM32262.1, CAM32261.1, CAM32260.1, CAM32259.1, CAM32258.1, CAM32257.1, CAM32256.1, CAM32255.1, CAM32254.1, CAM32253.1, CAM32252.1, CAM32251.1, CAM32249.1, 2LTH_B, 2LTH_A, AGQ04592.1, CAM32272.1, ACC77633.1, 4FBS_A, 2LPLA, 2LPI_A, ABR68856.1, ABR68855.1, ACF19416.1, ACF19415.1, ACF19414.1, ACF19413.1, ACF19412.1, ACF19411.1, AAZ15372.1, AAZ15321.1, AEV46833.2, CAM32271.1, CAM32270.1, CAJ90517.1, AAZ15371.1, AAZ15320.1, AAZ15322.1, AAT75317.1, AAT75316.1, AAT75315.1, AAT75314.1, AAT75313.1, AAT75312.1, AAT75311.1, AAT75310.1, AAT75309.1, AAT75308.1, ADV40100.1, AD078764.1, ADM14319.1, ADM14314.1, ABY67415.1, ABY67411.1, ABY67405.1, ABY67403.1, ABY67401.1, AAY28936.1, AAY28935.1, AAK30615.1, AAK30614.1, AAK30609.1, AAK30608.1, AAK30607.1, AAK30606.1, AAK30604.1, AAK30601.1, AAK30596.1, AAK30592.1, ADE74592.1, AAK30602.1, AAK30595.1, CAJ00428.1, ABY67429.1, ABY67428.1, ABY67427.1, ABY67426.1, ABY67425.1, ABY67424.1, ABY67423.1, ABY67422.1, ABY67421.1, ABY67420.1, ABY67419.1, ABY67418.1, ABY67417.1, ABY67414.1, ABY67412.1, ABY67410.1, ABY67408.1, ABY67406.1, ABY67404.1, ABY67402.1, ABY67400.1, ABR68858.1, ABR68857.1, NP_001149975.2, ABD24295.1, ABD24294.1, AAT08435.1, AAT08434.1, AAT08433.1, AAT08432.1, CAM32269.1, CAM32268.1, CAM32267.1, CAM32266.1, CAM32265.1, CAM32264.1, AJM90221.1, XP_013227994.1, EGF91682.1, ABY67416.1, ABY67413.1, ABY67409.1, ABY67407.1, AAK30605.1, AAK30603.1, AAK30597.1, AAK30591.1, KYK63513.1, KYK63505.1, KYF45748.1, LAA03183.1, LAA04613.1, LAA08218.1, LAA09714.1, LAA10141.1, LAA12328.1, LAA15428.1, LAA16019.1, LAA15714.1, LAA16712.1, XP_013439532.1, XP_013337057.1, XP_013248467.1, CEL74577.1, CEL67190.1, CBZ53200.1, KFH04906.1, KFH04893.1, KFH00791.1, KFG64992.1, KFG53453.1, KFG53436.1, KFG50409.1, KFG31363.1, ESS28619.1, CDJ62170.1, CDJ53902.1, CDJ36084.1, CDJ60407.1, CDI75130.1, CDJ37156.1, CDI81984.1, AFW71573.1, AFP64859.1, EMD82476.1, XP_003883232.1, EGY00935.1, EGY00136.1, EGY00025.1, EGY00024.1, EGY00023.1, EGY00022.1, EGY00021.1, EGX99920.1, ACG37383.1, CAM32250.1, 2MX9_B, 2MX9_A, 2MX8_A, 2MOM_B, 2MOM_A, AFN54363.1, AFV31615.1, AAN85281.1, AAR13814.1, AAR13813.1, AAR13812.1, AAR13811.1, AAR13810.1, AAR13809.1, AAR13808.1, AAR13807.1, AAR13806.1, 2MFZ_B, 2MFZ_A, AGB35874.1, AFN54362.1, ADM14322.1, ADM14320.1, ACB29694.1, AFM29836.1, ADM14328.1, ADM14326.1, ADM14321.1, ADM14317.1, ABC72644.1, AAP88232.1, ABR37275.1, AAX30096.1, ADM14318.1, 5IZ2_Z, 5IZ2_A, 5IZ2_B, 2MAB_B, 2MAB_A, AHK09813.1, ACF71409.1, ACF71408.1, AAC04504.1, AAC14590.1, AAC14589.1, AMK48677.1, AMK48676.1, AMK48674.1, AAC04503.1, ACF71410.1, ACF71407.1, ADM35668.1, ADM14332.1, ADM14330.1, ABC72645.1, AAY28945.1, AAY28943.1, AAY28942.1, AAY28940.1, AAY28939.1, AAY28934.1, AAX45292.1, AAV48953.1, AAV48952.1, AAV48951.1, AAV48950.1, AAV48949.1, AAV48948.1, AAV48947.1, AAV48946.1, AAV48945.1, AAV48944.1, AAV48940.1, AAV48939.1, AAV48938.1, AAV48937.1, AAV48936.1, AAV48935.1, AAV48934.1, AAV48933.1, AAV48932.1, AAV48931.1, AAV48930.1, AAV48929.1, AAV48928.1, AAV48927.1, AAV48926.1, AAV48925.1, AAV48924.1, AAV48923.1, AAV48922.1, AAV48921.1, AAV48920.1, AAR83925.1, AAL32472.1, AAC38957.1, ABR37276.1, AFX83565.1, AFX83563.1, AFX83561.1, AFX83560.1, AFX83559.1, AFX83558.1, AHK09789.1, AHK09788.1, AHK09787.1, AHK09786.1, AHK09785.1, AHK09784.1, AHK09783.1, AHK09782.1, AHK09781.1, AHK09780.1, AHK09779.1, AHK09778.1, AHK09777.1, AHK09776.1, AHK09775.1, AHK09774.1, AHK09773.1, AHK09772.1, AHK09771.1, AHK09770.1, AHK09769.1, AHK09768.1, AHK09767.1, AHK09766.1, AHK09765.1, AHK09764.1, AHK09763.1, AFX83566.1, AFX83557.1, ABD24296.1, 3LR2_B, 3LR2_A, P19837.3, P46802.1, P46804.1, 3LRD_B, 3LRD_A, 3LR8_B, 3LR8_A, 3LR6_B, 3LR6_A, XP_015337966.1, XP_015926902.1, XP_015923885.1, XP_015915953.1, XP_015907747.1, XP_015907077.1, XP_015907076.1, XP_015907075.1, XP_015907074.1, XP_015907073.1, XP_015907072.1, XP_015907071.1, XP_015907070.1, XP_015907069.1, XP_015927451.1, AMF13980.1, AMF13979.1, XP_005329120.1, KFM79920.1, KFM79313.1, KFM74936.1, BAE86855.1, ADG57595.1, AAB60212.1, AAA17673.1, WP_018592840.1, AAC88554.1, AAC81918.1, AOH90403.1, ADM14313.1, ABW80568.1, ABW80567.1, ABW80566.1, ABW80565.1, ABW80563.1, ABD61600.1, ABD61599.1, ABD61597.1, ABD61596.1, ABD61594.1, ABD61593.1, ABD61592.1, ABD61591.1, ABD61590.1, ABD61589.1, ABD61588.1, AAL32375.1, ADG57596.1, ADG57593.1, AAA29380.2, ABR37274.1, AAK30613.1, AAK30611.1, AAK30600.1, AAK30599.1, 2N3E_A, XP_007493712.1, XP_007493711.1, XP_007493710.1, XP_015924996.1, XP_015910086.1, XP_015910083.1, XP_015910082.1, XP_015910081.1, XP_015910080.1, XP_015908848.1, KYK65898.1, CUJ63677.1, KYF39742.1, KXJ25810.1, XP_006470793.1, XP_015337967.1, ALM54786.1, WP_054444469.1, WP_046811332.1, KL017202.1, AJQ48468.1, KFM60634.1, EPT32613.1, EIW81425.1, CAJ20380.1, WP_043737320.1, AJN51722.1, AJN51680.1, AJN51679.1, AJL53619.1, AJL53618.1, AJL53617.1, AJL53507.1, KIL96307.1, KGH32759.1, AIU80193.1, AIU51173.1, BAP74122.1, KFH16126.1, KFH14329.1, KFH03307.1, KFG59505.1, KFG53981.1, KFG48063.1, KFG46978.1, KFG35613.1, KFG31970.1, WP_031207438.1, XP_007768770.1, AHH59767.1, ESS29295.1, ERL52248.1, CDF00959.1, CDE91356.1, EPR57584.1, AGP17343.1, WP_016418412.1, EPC00821.1, WP_008485474.1, AGH61341.1, AGH61340.1, AGH61339.1, AGH61338.1, AGH61337.1, AGH61336.1, AGH61335.1, AGH61334.1, AGH61333.1, AGH61332.1, AGH61331.1, AGH61330.1, AGH61329.1, AGH61328.1, AGH61327.1, AGF22332.1, AGF22331.1, AGF22330.1, AFX03498.1, 2KHM_B, 2KHM_A, EKE71000.1, AFO02081.1, AFO02080.1, ADG57597.1, AFM97627.1, AFM97625.1, AFM97623.1, AFM97621.1, AFM97619.1, AFM97618.1, AFM97617.1, AFM97616.1, AFM97615.1, AFL33148.1, ABW80562.1, AAC47011.1, AAC47010.1, AAC47009.1, AAC47008.1, AAA29381.1, AEQ78099.1, AEQ78098.1, AEQ44307.1, AEQ44306.1, AEQ44305.1, AEH19948.1, AEH19947.1, AEH19946.1, ADS13223.1, ADS13222.1, ADS13221.1, ACR88286.1, ACR88284.1, ACR88282.1, ACR88281.1, ACR88277.1, ACR88276.1, ACR88274.1, ACR88272.1, ACR88270.1, ACR88269.1, ACR88268.1, ACR88267.1, ACR88266.1, ACR88265.1, ACR88264.1, ACR88263.1, BAE86856.1, AAE50748.1, 1589022, 1589021, BAE51681.1, AOH90437.1, AOH90431.1, NP_628424.1, ACI23395.1, ADH65296.1, ADH65027.1, AAC38846.1, AAF36091.1, XP_015928803.1, XP_015926099.1, XP_015926098.1, XP_015925523.1, XP_015922043.1, XP_015918918.1, XP_015913485.1, XP_015912961.1, XP_015912814.1, XP_015664484.1, XP_015664483.1, AMF14002.1, AMF14001.1, AMF13994.1, AMF13992.1, AMF13991.1, AMF13990.1, CUW39853.1, KPA86045.1, KPA86044.1, BAS78900.1, XP_013416068.1, WP_052004167.1, ADR37091.1, ENH87197.1, KFM79464.1, KFM73910.1, KFM70693.1, KFM62633.1, KFM62627.1, KFM61802.1, KFM61798.1, KFM59473.1, KFM57717.1, EPE04573.1, CAB77344.1, ADU51385.1, ADU51096.1, ADU50755.1, ADU50701.1, ADU50272.1, WP_028670286.1, AHL56647.1, ADK84021.1, WP_010403048.1, WP_011385254.1, AFX83556.1, EME70738.1, 2K3Q_A, AAR21194.1, AAX83289.1, XP_002462408.1, BAE54451.1, CAJ90517.1, AAC38846.1, AAF36091.1, AEQ78099.1, AEQ78098.1, ADH65317.1, ADH65186.1, EFP05295.1, XP_003113957.1, AFV31615.1, AFM29836.1, ADM14322.1, ADM14320.1, ADM14328.1, ADM14326.1, ADM14321.1, AFV31614.1, AFV31613.1, AFM29835.1, ADM14329.1, ADM14327.1, LAA15038.1, 2MOM_B, 2MOM_A, 2MX9_B, 2MX9_A, 2MX8_A, 2MFZ_B, 2MFZ_A, ACB29694.1, AAC14590.1, AAC14589.1, ABC72645.1, ABR37276.1, 2MAB_B, 2MAB_A, ADG57595.1, AAC88554.1, AAC81918.1, AMK48677.1, AMK48676.1, AMK48674.1, AMK48679.1, AMK48678.1, AMK48675.1, AMK48658.1, AMK48673.1, AMK48672.1, AMK48671.1, AMK48670.1, AMK48669.1, AMK48668.1, AMK48667.1, AMK48666.1, AMK48665.1, AMK48664.1, AMK48663.1, AMK48662.1, AMK48661.1, AMK48660.1, AMK48659.1, AFP57565.1, AFP57562.1, AFP57559.1, AAX45292.1, AAX45295.1, AAX45293.1, AAX45291.1, ANU43172.1, KOA64249.1, KOA59653.1, KOA54241.1, KOA52153.1, KOA48308.1, KOA44837.1, KOA44098.1, AJD89173.1, AJC77129.1, AGW85645.1, KFI80719.1, KFI77799.1, KFI56933.1, KFI41035.1, AIA33447.1, ACL28956.1, EHN17524.1, AAY28931.1, AAY28934.1, AAY28933.1, AAY28932.1, ADM14332.1, ADM14323.1, AAY28945.1, AAY28943.1, AAY28942.1, AAY28940.1, AAY28939.1, ADM14333.1, ADM14331.1, ADM14330.1, ABD24296.1, AAX45294.1, ADV40185.1, AAY28954.1, AAY28952.1, AAY28951.1, AAY28950.1, AAY28949.1, AAY28948.1, AAY28947.1, AAY28946.1, AAY28944.1, AAY28941.1, AAY28938.1, AAY28937.1, KFI66148.1, CDL70925.1, AFA43480.1, AAY28953.1, AFX83557.1, AAY28936.1, AAY28935.1, ABR68858.1, ABR68857.1, ABR37274.1, AFX83565.1, AFX83563.1, AFX83561.1, AFX83560.1, AFX83559.1, AFX83558.1, 2LYI_A, ABW24499.1, AFX83568.1, AFX83567.1, AFX83564.1, AFX83562.1, KFM79920.1, BAE86856.1, BAE86855.1, ABW80568.1, KFM62627.1, XP_015924996.1, XP_015907747.1, ABW80566.1, ABC72645.1, BAE54451.1, ABD61589.1, ABC72644.1, AAC14589.1, AAK30600.1, ACR88282.1, ACI23395.1, KFM70693.1, KFM62633.1, 2MAB_B, 2MAB_A, AAR83925.1, AHK09813.1, ADM35668.1, AFX83565.1, AFX83563.1, AFX83561.1, AFX83560.1, AFX83559.1, AFX83558.1, 2LYI_A, ABW24499.1, AHK09789.1, AHK09788.1, AHK09787.1, AHK09786.1, AHK09785.1, AHK09784.1, AHK09783.1, AHK09782.1, AHK09781.1, AHK09780.1, AHK09779.1, AHK09778.1, AHK09777.1, AHK09776.1, AHK09775.1, AHK09774.1, AHK09773.1, AHK09772.1, AHK09771.1, AHK09770.1, AHK09769.1, AHK09768.1, AHK09767.1, AHK09766.1, AHK09765.1, AHK09764.1, AHK09763.1, AFX83566.1, AFX83557.1, ADM35669.1, LAA01884.1, LAA09345.1, LAA09348.1, LAA15662.1, LAA16773.1, AHK09812.1, AHK09811.1, AHK09810.1, AHK09809.1, AHK09808.1, AHK09807.1, AHK09806.1, AHK09805.1, AHK09804.1, AHK09803.1, AHK09802.1, AHK09801.1, AHK09800.1, AHK09799.1, AHK09798.1, AHK09797.1, AHK09796.1, AHK09795.1, AHK09794.1, AHK09793.1, AFX83568.1, AFX83567.1, AFX83564.1, AFX83562.1, 2MU3_A, 307159084, 818905455, 347811351, 307159086, 307159082, and 301078347, the amino acid sequences corresponding to each accession number which are incorporated herein by reference.

In some embodiments, the silk fibroin domain comprises a minor ampullate silk fibroin domain. In some embodiments, the minor ampullate silk fibroin domain comprises an amino acid sequence as set forth in NCBI Database Accession Numbers: AAC14589.1, AAC14590.1, AAC14591.1, A0034847.1, A0034825.1, ACI63001.1, AIT41471.1, AGX00072.1, AGX00067.1, AGX00064.1, AGX00062.1, AGP47431.1, AGP47492.1, AG088936.1, AG088929.1, AG088926.1, AG088855.1, AG088848.1, AG088845.1, AAK62518.1, CUU33208.1, CUI09422.1, AJR18647.1, YP_008166902.1, YP_008161883.1, CTQ89448.1, CEL20537.1, YP_009062955.1, YP_009062950.1, YP_009062947.1, YP_009062945.1, YP_009023249.1, YP_009023242.1, YP_009023239.1, YP_009023168.1, YP_009023161.1, YP_009023158.1, NP_862422.1, YP_008145026.1, YP_002286943.1, CEF90318.1, CDF32058.1, 2MX9_B, 2MX9_A, 2MX8_A, 2MOM_B, 2MOM_A, 2MFZ_B, 2MFZ_A, ACB29694.1, AFV31615.1, ABC72645.1, ABR37276.1, ABR37278.1, ADM14328.1, ADM14326.1, ADM14321.1, ABR37277.1, ADM14322.1, ADM14320.1, ADM14329.1, ADM14327.1, 2MAB_B, 2MAB_A, ADG57595.1, AAC88554.1, AAC81918.1, 2MQA_A, AAC88595.1, AAC88594.1, AAC88593.1, AAC88592.1, AAC88591.1, AAC88590.1, AAC88589.1, AAC88588.1, AAC88587.1, AAC88586.1, AAC88585.1, AAC88584.1, AAC88583.1, AAC88582.1, AAC88581.1, AAC88580.1, AAC88579.1, AAC88578.1, AAC88577.1, AAC88576.1, AAC88575.1, AAC88574.1, AAC88573.1, AAC88572.1, AAC88571.1, AAC88570.1, AAC88569.1, AAC88568.1, AAC88567.1, AAC88566.1, AAC88565.1, AAC88564.1, AAC88563.1, AAC88562.1, AAC88561.1, AAC88560.1, AAC88559.1, AAC88558.1, AAC88557.1, AAC88556.1, AAC88555.1, AAC88553.1, AAC88552.1, AAC88551.1, AAC81959.1, AAC81958.1, AAC81957.1, AAC81956.1, AAC81955.1, AAC81954.1, AAC81953.1, AAC81952.1, AAC81951.1, AAC81950.1, AAC81949.1, AAC81948.1, AAC81947.1, AAC81946.1, AAC81945.1, AAC81944.1, AAC81943.1, AAC81942.1, AAC81941.1, AAC81940.1, AAC81939.1, AAC81938.1, AAC81937.1, AAC81936.1, AAC81935.1, AAC81934.1, AAC81933.1, AAC81932.1, AAC81931.1, AAC81930.1, AAC81929.1, AAC81928.1, AAC81927.1, AAC81926.1, AAC81925.1, AAC81924.1, AAC81923.1, AAC81922.1, AAC81921.1, AAC81920.1, AAC81919.1, AAC81917.1, AAC81916.1, and AAC81915.1, the amino acid sequences corresponding to each accession number which are incorporated herein by reference.

In some embodiments, the silk fibroin domain comprises an aggregate silk fibroin domain. In some embodiments, the aggregate silk fibroin domain comprises an amino acid sequence as set forth in NCBI Database Accession Numbers: AMK48658.1, AMK48673.1, AMK48672.1, AMK48671.1, AMK48670.1, AMK48669.1, AMK48668.1, AMK48667.1, AMK48666.1, AMK48665.1, AMK48664.1, AMK48663.1, AMK48662.1, AMK48661.1, AMK48660.1, AMK48659.1, AFP57565.1, AFP57562.1, AMK48679.1, AMK48678.1, AMK48677.1, AMK48676.1, AMK48675.1, and AMK48674.1, the amino acid sequences corresponding to each accession number which are incorporated herein by reference.

In some embodiments, the silk fibroin domain comprises a flagelliform (flag) silk fibroin domain. In some embodiments, the flagelliform (flag) silk fibroin domain comprises an amino acid sequence as set forth in NCBI Database Accession Numbers: AAC38846.1, AAT36347.1, AAC38847.1, AAF36091.1, AAK30594.1, AAK30593.1, AAF36092.1, AAF36090.1, AAF36089.1, EEC09351.1, EEC05390.1, ADN23579.1, ADN23577.1, KUG05367.1, AIY48668.1, CTQ93180.1, CRK58766.1, CRK58764.1, AJW39886.1, BAQ62602.1, KKW05526.1, EEC20124.1, EAX93621.1, CEL23644.1, KIG11542.1, EWC62749.1, EUA21042.1, EJI95902.1, XP_002433990.1, XP_002400080.1, XP_002401328.1, XP_001306551.1, BAC99451.1, ABR37273.1, ABK00016.1, CAJ90517.1, ADH65223.1, ADH65221.1, ADH65090.1, ADH65055.1, ADH65034.1, BAS78003.1, ADV61483.1, AEB08848.1, ADU52289.1, ADU51393.1, BAF18870.1, BAF08409.1, BAG95178.1, and CAB87946.1, the amino acid sequences corresponding to each accession number which are incorporated herein by reference.

In some embodiments, the silk fibroin domain is a tubulin silk fibroin domain. In some embodiments, the tubulin silk fibroin domain comprises an amino acid sequence as set forth in NCBI Database Accession Numbers: JAR06716.1, BAE86856.1, BAE86855.1, AAY28931.1, 2K3O_A, 2K3N_A, AAY28933.1, AAY28932.1, BAE54450.1, AAY28934.1, AAX45295.1, AAX45293.1, AAX45291.1, BAE54451.1, ABR37274.1, ACI23395.1, ADM14323.1, ABD24296.1, ADM14332.1, AAX45292.1, AAC14589.1, ADV40185.1, ADM14333.1, ADM14331.1, AAY28954.1, AAY28952.1, AAY28951.1, AAY28950.1, AAY28949.1, AAY28948.1, AAY28947.1, AAY28946.1, AAY28945.1, AAY28944.1, AAY28943.1, AAY28942.1, AAY28941.1, AAY28940.1, AAY28939.1, AAY28938.1, AAY28937.1, ADM14330.1, AAX45294.1, AFA43480.1, AAY28953.1, KFM79920.1, AFX83557.1, AGR65217.1, WP_020843129.1, AFM97620.1, ABW80568.1, KFM62627.1, AAZ15706.1, AAK30612.1, ACR88285.1, ABD61598.1, AAY90151.1, ABR68858.1, ABR68857.1, ABW80564.1, AAY28936.1, AAY28935.1, ABD61589.1, XP_015924996.1, KXT76149.1, ABW80566.1, ABC72645.1, ABN13925.1, XP_015907747.1, ABR37278.1, CUR40212.1, KTF81708.1, XP_014025605.1, XP_014025604.1, XP_014025602.1, ABW24499.1, ADV40181.1, ABC72644.1, AAK30600.1, KFM70693.1, KFM62633.1, AHK09791.1, AFX83568.1, AFX83567.1, AFX83565.1, AFX83564.1, AFX83563.1, AFX83562.1, AFX83561.1, AFX83560.1, AFX83559.1, AFX83558.1, ACR88282.1, EOY18426.1, ADU23756.1, EAQ83169.1, ACV03419.1, EDW00619.1, KZN71099.1, WP_062906493.1, WP_062896115.1, ALU60113.1, XP_006990705.2, KXZ53453.1, KXT17944.1, KXJ08739.1, XP_015495616.1, XP_015472967.1, XP_015472966.1, XP_015472964.1, XP_015472963.1, XP_015472962.1, XP_015472961.1, CUR39570.1, XP_015338007.1, XP_015338006.1, GAC97239.1, XP_002000489.1, CUU27780.1, XP_014781761.1, XP_014773071.1, XP_014794002.1, XP_014794001.1, XP_014794000.1, XP_014726746.1, XP_014726745.1, XP_014726744.1, WP_011723794.1, CUI03994.1, WP_057406778.1, EDW15950.1, KPX62564.1, XP_008545413.1, KPI97631.1, WP_054263331.1, XP_014167486.1, XP_014116011.1, XP_014122317.1, XP_014122316.1, XP_014112343.1, XP_014030156.1, XP_014030155.1, XP_014030153.1, XP_014025603.1, XP_014054492.1, XP_013676349.1, KOF87513.1, KOF87511.1, WP_050780405.1, WP_042229582.1, WP_051870755.1, WP_051863026.1, WP_051861131.1, KEQ92117.1, XP_013340518.1, XP_013227263.1, XP_013227262.1, XP_013227261.1, XP_013153866.1, XP_005463415.1, CRH97187.1, XP_013034801.1, XP_012994535.1, XP_012994534.1, XP_012994533.1, XP_012994532.1, XP_012950187.1, XP_012950183.1, 2 MQA_A, XP_012670522.1, AKI80407.1, WP_046357626.1, KKE81922.1, XP_012190826.1, KFM77639.1, EKX40791.1, EGX96200.1, XP_011413944.1, CEK40236.1, XP_011315453.1, JAG80700.1, K1M38534.1, CAQ41616.1, WP_036204683.1, KHN36369.1, CCQ38052.1, XP_010005229.1, CDY50596.1, CDG98384.1, CDH00697.1, CDH18149.1, WP_030453286.1, KEQ48985.1, CDP19197.1, WP_026128052.1, WP_024859189.1, AGR65376.1, XP_007910174.1, XP_007905153.1, YP_008873468.1, EYB28497.1, AGI11726.1, XP_006818343.1, XP_006807688.1, XP_006807687.1, XP_006807686.1, ABK65722.1, XP_006666077.1, XP_005827771.1, WP_021434916.1, EQK53805.1, WP_018500291.1, WP_010166019.1, WP_015410778.1, WP_013483306.1, 2 LYI_A, YP_001426738.1, XP_001985752.1, EFA85813.1, XP_002260349.1, XP_001613854.1, XP_001226254.1, ABT16391.1, and EDL44127.1, the amino acid sequences corresponding to each accession number which are incorporated herein by reference.

In some embodiments, the silk fibroin domain is an aciniform silk fibroin domain. In some embodiments, the aciniform silk fibroin domain comprises an amino acid sequence as set forth in NCBI Database Accession Numbers: AFX83557.1, 2MU3_A, 2MAB_B, 2MAB_A, ABW24499.1, AAR83925.1, AHK09813.1, AHK09791.1, AHK09789.1, AHK09788.1, AHK09787.1, AHK09786.1, AHK09785.1, AHK09784.1, AHK09783.1, AHK09782.1, AHK09781.1, AHK09780.1, AHK09779.1, AHK09778.1, AHK09777.1, AHK09776.1, AHK09775.1, AHK09774.1, AHK09773.1, AHK09772.1, AHK09771.1, AHK09770.1, AHK09769.1, AHK09768.1, AHK09767.1, AHK09766.1, AHK09765.1, AHK09764.1, AHK09763.1, AFX83568.1, AFX83567.1, AFX83566.1, AFX83565.1, AFX83564.1, AFX83563.1, AFX83562.1, AFX83561.1, AFX83560.1, AFX83559.1, AFX83558.1, 2LYI_A, AHK09812.1, AHK09811.1, AHK09810.1, AHK09809.1, AHK09808.1, AHK09807.1, AHK09806.1, AHK09805.1, AHK09804.1, AHK09803.1, AHK09802.1, AHK09801.1, AHK09800.1, AHK09799.1, AHK09798.1, AHK09797.1, AHK09796.1, AHK09795.1, AHK09794.1, AHK09793.1, AHK09792.1, and AHK09790.1, the amino acid sequences corresponding to each accession number which are incorporated herein by reference.

In some embodiments, the silk fibroin domain is a piriform silk fibroin domain. In some embodiments, the piriform silk fibroin domain comprises an amino acid sequence as set forth in NCBI Database Accession Numbers: AEP25627.1, ADN39427.1, ADN39425.1, ADN39426.1, and ADK56477.1, the amino acid sequences corresponding to each accession number which are incorporated herein by reference.

Methods of the present invention use the curli fiber production systems of a bacterium, such as E. coli to produce collagen protein or curli fibers formed using recombinant silk or collagen proteins described herein that comprise an amyloid domain (e.g., CsgA).

Curli fibers are the primary proteinaceous structural component of E. coli biofilms. They are highly robust functional amyloid nanofibers with a diameter of approximately 4-7 nm that exist as extended tangled networks encapsulating the cells. Curli fibers or curli are formed from the extracellular self-assembly of CsgA, a small secreted 13-kDa protein (see, e.g., Chapman, M. R. et al. Role of Escherichia coli curli operons in directing amyloid fiber formation. Science 295, 851-855 (2002)). A homologous outer-membrane protein, CsgB, nucleates CsgA assembly and also anchors the nanofibers to the bacterial surface. Detached curli fibers can also exist as non-cell associated structural components of the extracellular matrix (ECM). The curli genes exist as two divergently transcribed operons (csgBAC and csgDEFG), whose seven products mediate the structure (CsgA), nucleation (CsgB), processing (CsgE, F), secretion (CsgC, G), and direct transcriptional regulation (CsgD) of curli nanofibers. This curli secretion system is considered a distinct secretion system of its own in gram-negative bacterium and is named the Type-VIII secretion system (T8SS) (see, e.g., Desvaux et al., Trends Microbiol. 17, 139-45 (2009), which is hereby incorporated by reference in its entirety). Thus, in some embodiments, the heterologous nucleic acid encoding a recombinant silk or collagen protein further comprises a heterologous nucleic acid encoding an amyloid domain. In some embodiments, the recombinant silk or collagen protein further comprises an amyloid domain. In some embodiments, the amyloid domain comprises CsgA.

Aspects of the present disclosure are directed to the use of a secretion system, such as a T8SS secretion system, to export a recombinant silk polypeptide disclosed herein, such as a recombinant silk protein comprising a spider silk fibroin domain or a recombinant collagen protein comprising one or more V′ and/or CL domains of bacterial collagen, from within a bacterium (such as a gram-negative or gram-positive bacterium) and into the surrounding environment. According to one aspect, the recombinant silk or collagen protein is an amyloid hybrid, for example, which comprises a silk fibroin domain or collagen domain connected (i.e., fused) to an amyloid domain (e.g., CsgA). According to this aspect, the recombinant protein is secreted into the extracellular space or milieu (e.g., medium) of the bacterium. The secreted recombinant protein can then be collected and purified. Alternatively, the recombinant protein is not fused to an amyloid domain and is secreted into the extracellular medium where it can be collected, processed, isolated, and/or purified by methods known in the art. According to one aspect, the recombinant silk protein can comprise one or more of an amyloid, elastin, or collagen domains to alter the physical and mechanical properties of the resulting material as compared to a recombinant silk protein that does not comprise an amyloid, elastin, or collagen domain.

In one aspect, provided herein is an engineered bacterium comprising a heterologous nucleic acid sequence encoding a recombinant silk protein, wherein the recombinant silk protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, a silk fibroin domain and one or more of an amyloid domain, an elastin domain or a collagen domain. In some embodiments, the amyloid domain is CsgA.

In another aspect, provided herein is a nucleic acid sequence encoding a recombinant silk protein described herein. In one embodiment, provided herein is a nucleic acid sequence encoding a recombinant silk protein, wherein the recombinant silk protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, a silk fibroin domain and one or more of an amyloid domain, an elastin domain or a collagen domain. In some embodiments, the amyloid domain is CsgA.

In yet another aspect, provided herein is a recombinant silk protein comprising a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, a silk fibroin domain and one or more of an amyloid domain, an elastin domain or a collagen domain. In some embodiments, the periplasmic translocation signal sequence and/or the outer membrane secretion signal sequence is cleaved-off the recombinant silk protein within the cell. In some embodiments, the amyloid domain is CsgA.

As used herein, “CsgA” refers to the major structural subunit of curli. The sequences of CsgA and its homologs are known in a number of species, e.g., the sequence of E. coli CsgA is known (NCBI Gene ID NO: 949055; (SEQ ID NO: 4) (polypeptide)).

CsgA polypeptide (NCBI Ref Seq: NP_415560)

(SEQ ID NO: 4)   1 mkllkvaaia aivfsgsala gvvpqygggg nhggggnnsg pnselniyqy gggnsalalq  61 tdarnsdlti tqhgggngad vgqgsddssi dltqrgfgns atldqwngkn semtvkqfgg 121 gngaavdqta snssvnvtqv gfgnnatahq y.

In some embodiments, “CsgA” refers to an E. coli CsgA. In some embodiments, “CsgA” refers to a polypeptide having at least 80% homology to SEQ ID NO: 4 (e.g., 80% or greater homology, 90% or greater homology, or 95% or greater homology), e.g. naturally occurring mutations or variants of CsgA, homologs of CsgA, or engineered mutations or variants of CsgA. In some embodiments, CsgA refers to a polypeptide comprising an amino acid sequence having at least 80%, 81%, 82%, 83% 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the amino acid sequence of SEQ ID NO: 4. The silk fibroin domain may be directly connected to the CsgA polypeptide or be connected via a linker at either the C-terminus or the N-terminus or both of the CsgA, but without interrupting the sequence of the CsgA polypeptide. CsgA within the scope of the present disclosure includes an amyloid domain which self-assembles into an amyloid structure. According to certain aspects, a linker may be attached to either the C-terminus or the N-terminus or separate linkers may be attached to both the C terminus and the N terminus of the CsgA.

According to one aspect, self-assembling protein domains, such as CsgA, are used to generate the similar self-assembling characteristics for artificial silk or collaten fusion proteins. A factor in the maturation of spider silk in spiders is the self-assembly of N- and C-terminal domains initiated by changes in pH and ionic strength (see, e.g., Gronau et al. (2013) Biomater. Sci. 1(3): 276-84; Hagn et al. (2010) Nature 465(7295): 239-42; Schwarze et al. (2013) Nat. Commun. 4: 2815). These changes in the spider's silk glands lead to the step-wise assembly of the silk proteins from a stored nematic liquid to a super strong biofilament. Replicating this assembly of the silk proteins into a strong fiber has been a key step towards replicating the amazing physical properties of spider silk. According to the present disclosure, the pH/salt driven assembly of the N- and C-terminal domains is replaced with other self-assembling protein domains, such as CsgA, to generate the similar self-assembling characteristics for artificial silk fusion proteins.

According to one aspect, engineered bacteria are modified to comprise a heterologous nucleic acid encoding the recombinant protein described herein (e.g., a recombinant collagen protein, or a recombinant silk protein comprising an amyloid domain such as CsgA). In some embodiments, the recombinant silk protein comprises an elastin domain or a collagen domain. Useful sequences and structures for elastin domains and collagen domains are known to those of skill in the art, such as VPVXG (SEQ ID NO: 5) which is an exemplary elastin domain.

The polypeptide, e.g., collagen or spider silk, may also be connected to a domain which guides the polypeptide to the periplasm and/or a domain which guides the polypeptide outside of the bacterium through the outer cell wall. Methods of introducing a nucleic acid to a bacteria cell are known to those of skill in the art. In some embodiments, the engineered bacterium is modified to comprise a heterologous nucleic acid encoding a recombinant protein described herein, wherein the heterologous nucleic acid is located in the bacterial chromosome. In some embodiments, the engineered bacterium is modified to comprise a heterologous nucleic acid encoding a recombinant silk protein described herein, wherein the heterologous nucleic acid is located in a plasmid.

According to one aspect, the engineered bacteria secrete the recombinant protein (e.g., collagen or silk), such that the protein is free for collection and purification. According to one aspect, the modified bacteria secrete the recombinant protein resulting in curli fiber production. In another aspect, provided herein are biofilms, hydrogels and triple-helical fiber meshworks comprising the recombinant proteins described herein, or an engineered bacteria described herein are provided.

In some embodiments, the recombinant protein (e.g., recombinant spider silk, collagen or recombinant CsgA-fusions thereof) may be produced by engineered or non-naturally occurring bacteria. According to one aspect, methods are provided for engineering a bacteria to produce a recombinant protein (e.g., a recombinant silk or collagen protein not comprising an amyloid domain or a recombinant silk or collagen protein comprising an amyloid domain) which may be exported from the bacterium. The recombinant silk protein comprising an amyloid domain (e.g., CsgA, which is also referred to herein as a CsgA-spider silk fusion protein) may be exported from the bacterium and assemble into extracellular amyloid fibers. After secretion, the CsgA-spider silk fusion protein may be nucleated to form an amyloid at the cell surface, polymerize into long fibers, and optionally, eventually encapsulate the bacterium, and provide a biofilm with structural support. In some embodiments, provided herein are biofilms comprising an engineered bacterium as described herein.

CsgA within the scope of the present disclosure includes an amyloid domain which self-assembles into an amyloid structure. According to certain aspects, a linker may be attached to either the C terminus or the N-terminus or separate linkers may be attached to both the C terminus and the N terminus.

Aspects of the present disclosure are directed to a method of producing a genetically modified bacterium including genetically altering a bacterium having one or more genomic nucleic acids encoding a polypeptide secretion system to include an exogenous nucleic acid encoding a recombinant protein including a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and one or more silk fibroin or collagen domains, wherein the exogenous nucleic acid is under operation of a promoter to express the recombinant protein. According to one aspect, the polypeptide secretion system is a Type VIII secretion system or a HlyA Type 1 secretion system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a Sec system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a twin-arginine translocation (Tat) system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a signal recognition particle (SRP) system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a Sec domain or a Tat domain or a signal recognition particle domain. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a component of a Sec system, a component of a Tat system or a component of a signal recognition particle system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a N22 system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a YebF system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein a domain for directing the recombinant protein to the outer membrane for secretion is an N22 domain or a YebF domain. According to one aspect, the exogenous nucleic acid further encodes one or more curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. In some embodiments, the exogenous nucleic acid further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include one or more of an amyloid domain, an elastin domain or a collagen domain. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include a CsgA domain. According to one aspect, the bacterium is E. coli. According to one aspect, the bacterium is non-pathogenic. According to one aspect, the silk fibrin domain includes the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). According to one aspect, the silk fibrin domain includes 4 to 64 repeats of the amino acid sequence

(SEQ ID NO: 3) GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS.

According to one aspect, the collagen domain comprises one or more V′ domains comprising the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075) and/or one or more CL domains comprising the amino acid sequence GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRGLQGERGE QGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGEAGAQGPAGPMGPA GERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPAGKDGERGPVGPAGKDGQNG QDGLPGKDGKDGQNGKDGLPGKDGKDGQNGKDGLPGKDGKDGQDGKDGLPGKD GKDGLPGKDGKDGQPGKP (SEQ ID NO: 2076). In some embodiments, the collagen domain comprises a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions.

Aspects of the present disclosure are directed to a method for producing one or more silk fibroin domains or one or more collagen domains from a genetically modified bacterium including providing the genetically modified bacterium in culture media conditions, wherein the genetically modified bacterium includes one or more genomic nucleic acids encoding a polypeptide secretion system and further including an exogenous nucleic acid encoding a recombinant protein including a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and the one or more silk fibroin or collagen domains, wherein the exogenous nucleic acid is under operation of a promoter to express the recombinant protein, and expressing the exogenous nucleic acid to produce the recombinant protein wherein the recombinant protein is secreted from the bacterium and into the surrounding culture media. According to one aspect, the method further provides proliferating the bacterium to produce a population of bacteria cells expressing the exogenous nucleic acid. According to one aspect, the method further provides proliferating the bacterium to produce a population of bacteria cells expressing the exogenous nucleic acid to form a biofilm including the recombinant protein. According to one aspect, the polypeptide secretion system is a Type VIII secretion system or a HlyA Type 1 secretion system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a Sec system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a twin-arginine translocation (Tat) system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a signal recognition particle (SRP) system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a Sec domain or a Tat domain or a signal recognition particle domain. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a component of a Sec system, a component of a Tat system or a component of a signal recognition particle system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a N22 system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a YebF system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein a domain for directing the recombinant protein to the outer membrane for secretion is an N22 domain or a YebF domain. According to one aspect, the exogenous nucleic acid further encodes one or more curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. In some embodiments, the exogenous nucleic acid further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include one or more of an amyloid domain, an elastin domain or a collagen domain. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include a CsgA domain. According to one aspect, the bacterium is E. coli. According to one aspect, the bacterium is non-pathogenic. According to one aspect, the silk fibrin domain includes the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). According to one aspect, the silk fibrin domain includes 4 to 64 repeats of the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO: 3). According to one aspect, the collagen domain comprises one or more V′ domains comprising the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075) and/or one or more CL domains comprising the amino acid sequence GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRGLQGERGE QGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGEAGAQGPAGPMGPA GERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPAGKDGERGPVGPAGKDGQNG QDGLPGKDGKDGQNGKDGLPGKDGKDGQNGKDGLPGKDGKDGQDGKDGLPGKD GKDGLPGKDGKDGQPGKP (SEQ ID NO: 2076). In some embodiments, the collagen domain comprises a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions.

According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins comprising an enzyme, an antibody or a detectable protein. According to one aspect, the recombinant protein is unattached to the bacterium. According to one aspect, the recombinant protein is attached to the bacterium.

Aspects of the present disclosure are directed to a genetically modified bacterium including one or more genomic nucleic acids encoding a polypeptide secretion system and further including an exogenous nucleic acid encoding a recombinant protein including a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and one or more silk fibroin or collagen domains, wherein the exogenous nucleic acid is under operation of a promoter to express the recombinant protein. According to one aspect, the polypeptide secretion system is a Type VIII secretion system or a HlyA Type 1 secretion system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a Sec system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a twin-arginine translocation (Tat) system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the periplasmic secretion system is a signal recognition particle (SRP) system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a Sec domain or a Tat domain or a signal recognition particle domain. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and a domain for periplasmic localization is a component of a Sec system, a component of a Tat system or a component of a signal recognition particle system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a N22 system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein the system for secretion through the outer membrane of the bacterium is a YebF system. According to one aspect, the polypeptide secretion system includes a periplasmic secretion system and a system for secretion through the outer membrane of the bacterium and wherein a domain for directing the recombinant protein to the outer membrane for secretion is an N22 domain or a YebF domain. According to one aspect, the exogenous nucleic acid further encodes one or more curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. In some embodiments, the exogenous nucleic acid further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include one or more of an amyloid domain, an elastin domain or a collagen domain. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include a CsgA domain. According to one aspect, the bacterium is E. coli. According to one aspect, the bacterium is non-pathogenic. According to one aspect, the silk fibrin domain includes the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO:3). According to one aspect, the silk fibrin domain includes 4 to 64 repeats of the amino acid sequence GRGGLGGQGAGMAAAAAMGGAGQGGYGGLGSQGTS (SEQ ID NO:3). According to one aspect, the collagen domain comprises one or more V′ domains comprising the amino acid sequence DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQEREQAEN SWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075) and/or one or more CL domains comprising the amino acid sequence GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRGLQGERGE QGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGEAGAQGPAGPMGPA GERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPAGKDGERGPVGPAGKDGQNG QDGLPGKDGKDGQNGKDGLPGKDGKDGQNGKDGLPGKDGKDGQDGKDGLPGKD GKDGLPGKDGKDGQPGKP (SEQ ID NO: 2076). In some embodiments, the collagen domain comprises a V′ domain, an intervening trypsin-sensitive region, and a CL domain. In some embodiments, the recombinant collagen comprises one or more CL domains. In some embodiments, the one or more CL domains include one or more trypsin-sensitive regions.

According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins. According to one aspect, the exogenous nucleic acid further encodes the recombinant protein to include one or more functional proteins comprising an enzyme, an antibody or a detectable protein. According to one aspect, the recombinant protein is unattached to the bacterium. According to one aspect, the recombinant protein is attached to the bacterium.

In some embodiments, the heterologous nucleic acid encoding a recombinant silk or collagen protein further comprises a heterologous nucleic acid encoding a functional protein. In some embodiments, the heterologous nucleic acid encoding a recombinant silk or collagen protein further comprises one or more (e.g., two, three, four, five, six, or more) heterologous nucleic acid encoding a functional protein. In some embodiments, the recombinant protein further comprises a functional protein domain (e.g., the recombinant silk or collagen protein is fused to a functional protein described herein). In some embodiments, the recombinant protein comprises one or more (e.g., two, three, four, five, six, or more) functional proteins. In some embodiments, the functional protein comprises an enzyme, an antibody, a detectable protein, or a fragment thereof. In some embodiments, the detectable protein is a poly-histidine tag, a myc tag a FLAG tag, a hemagglutinin (HA) tag, or a V5 tag.

In some embodiments, the heterologous nucleic acid encoding the recombinant protein further comprises a heterologous nucleic acid encoding a protease cleavage site amino acid sequence. In some embodiments, the recombinant protein further comprises a protease cleavage site amino acid sequence. The protease cleavage site amino acid sequence may be disposed at any location between the multiple domains of the recombinant protein, including for example: between a periplasmic translocation signal sequence and an outer membrane secretion signal sequence, between an outer membrane secretion signal sequence and a silk fibroin or bacterial collagen domain, between a bacterial collagen V′ domain and CL domain, between two or more CL domains, between a periplasmic translocation signal sequence and a silk fibroin or bacterial collagen domain, between an outer membrane secretion signal sequence and an amyloid domain, between a periplasmic translocation signal sequence and an amyloid domain, between a first silk fibroin domain and a second silk fibroin domain, between a silk fibroin or bacterial collagen domain and an amyloid domain, between an amyloid domain and a functional protein, between a silk fibroin or bacterial collagen domain and a functional protein. In some such embodiments, the cleavage site is a trypsin sensitive region.

In some embodiments, the heterologous nucleic acid encoding a recombinant silk protein further comprises a heterologous nucleic acid encoding a linker sequence. In some embodiments, the recombinant protein further comprises a linker sequence. The linker sequence may be disposed at any location between the multiple domains of the recombinant protein, including for example: between a periplasmic translocation signal sequence and an outer membrane secretion signal sequence, between an outer membrane secretion signal sequence and a silk fibroin or bacterial collagen domain, between a periplasmic translocation signal sequence and a silk fibroin or bacterial collagen domain, between a first silk fibroin or bacterial collagen domain and a second silk fibroin or bacterial collagen domain, between a silk fibroin or bacterial collagen domain and an amyloid domain, between an amyloid domain and a functional protein, between a silk fibroin or bacterial collagen domain and a functional protein.

Aspects of the present disclosure are directed to a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or bacterial collagen domains.

Aspects of the present disclosure are directed to a nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

Aspects of the present disclosure are directed to a vector comprising a nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

In one aspect, described herein are vectors comprising a heterologous nucleic acid described herein (e.g., a heterologous nucleic acid encoding a recombinant protein (e.g., recombinant silk or collagen protein), wherein the recombinant protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, a silk fibroin or collagen domain, and optionally, one or more of an amyloid domain, and an elastin domain).

Aspects of the present disclosure are directed to a bacterium including a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

Aspects of the present disclosure are directed to a bacterium including a vector comprising a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

Aspects of the present disclosure are directed to a bacterium expressing a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

Aspects of the present disclosure are directed to a biofilm including a bacterium expressing a foreign or exogenous nucleic acid sequence encoding a non-naturally occurring protein including a fusion of a domain for periplasmic localization of the protein to periplasm of a bacterium, a domain for directing the protein to the outer membrane of a bacterium for secretion and one or more silk fibroin or collagen domains.

A “vector” includes a nucleic acid construct designed for delivery to a host cell or transfer between different host cells (e.g., a bacterial cell described herein). A vector can be viral or non-viral. Many vectors useful for transferring genes into target cells are available, e.g., the vectors may be episomal, e.g., plasmids, virus-derived vectors, or may be integrated into the target cell genome, through homologous recombination or random integration.

In some embodiments, a vector can be an expression vector. An “expression vector” can be a vector that has the ability to incorporate and express heterologous nucleic acid fragments in a cell. An expression vector may comprise additional elements, for example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms. The nucleic acid incorporated into the vector can be operably-linked to an expression control sequence when the expression control sequence controls and regulates the transcription and translation of that polynucleotide sequence.

In some embodiments, a heterologous nucleic acid encoding a recombinant protein (e.g., recombinant silk or collagen protein), wherein the recombinant protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, and a silk fibroin or collagen domain; or a nucleic acid encoding a recombinant protein including one or more silk fibroin or collagen domains and one or more of a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion, or a functional polypeptide such as an amyloid domain, or an elastin domain; can be present within a portion of a plasmid. Plasmid vectors include, but are not limited to, pBR322, pBR325, pACYC177, pACYC184, pUC8, pUC9, pUC18, pUC19, pLG339, pR290, pKC37, pKC101, SV 40, pBluescript II SK+/− or KS+/−(see “Stratagene Cloning Systems” Catalog (1993) from Stratagene, La Jolla, Calif., which is hereby incorporated by reference), pQE, pIH821, pGEX, pET series (see Studier et al., “Use of T7 RNA Polymerase to Direct Expression of Cloned Genes,” Gene Expression Technology, vol. 185 (1990), which is hereby incorporated by reference in its entirety).

A “viral vector” may be a nucleic acid vector construct that includes at least one element of viral origin and has the capacity to be packaged into a viral vector particle. The viral vector can contain a transgenic gene in place of non-essential viral genes. The vector and/or particle may be utilized for the purpose of transferring any nucleic acids into cells either in vitro or in vivo. Numerous viral vectors are known in the art and can be used as carriers of a nucleic acid into a cell, e.g. lambda vector system gt11, gt WES.tB, Charon 4.

In some embodiments, a heterologous nucleic acid described herein; such as a nucleic acid encoding a recombinant protein including one or more silk fibroin or collagen domains and one or more of a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion, or a functional polypeptide such as an amyloid domain, or an an elastin domain; can be constitutively expressed. In some embodiments, a heterologous nucleic acid described herein can be operably-linked to a constitutive promoter. In some embodiments, the heterologous nucleic acid described herein can be inducibly-expressed. In some embodiments, the heterologous nucleic acid described herein can be operably linked to an inducible promoter. In some embodiments, the heterologous nucleic acid described herein can be operably-linked to a native CsgA promoter.

An “inducible promoter” may be one that is characterized by initiating or enhancing transcriptional activity when in the presence of, influenced by, or contacted by an inducer or inducing agent than when not in the presence of, under the influence of, or in contact with the inducer or inducing agent. An “inducer” or “inducing agent” may be endogenous, or a normally exogenous compound or protein that is administered in such a way as to be active in inducing transcriptional activity from the inducible promoter. In some embodiments, the inducer or inducing agent, e.g., a chemical, a compound or a protein, can itself be the result of transcription or expression of a nucleic acid sequence (e.g., an inducer can be a transcriptional repressor protein), which itself may be under the control or an inducible promoter. Non-limiting examples of inducible promoters include but are not limited to, the lac operon promoter, a nitrogen-sensitive promoter, an IPTG-inducible promoter, a salt-inducible promoter, and tetracycline, steroid-responsive promoters, rapamycin responsive promoters and the like. Inducible promoters for use in prokaryotic systems are well known in the art, see, e.g., the beta-lactamase and lactose promoter systems (Chang et al., Nature, 275: 615 (1978), which is incorporated herein by reference); Goeddel et al., Nature, 281: 544 (1979), which is incorporated herein by reference), the arabinose promoter system, including the araBAD promoter (Guzman et al., J. Bacteriol., 174: 7716-7728 (1992), which is incorporated herein by reference; Guzman et al., J. Bacteriol., 177: 4121-4130 (1995), which is incorporated herein by reference; Siegele and Hu, Proc. Natl. Acad. Sci. USA, 94: 8168-8172 (1997), which is incorporated herein by reference), the rhamnose promoter (Haldimann et al., J. Bacteriol., 180: 1277-1286 (1998), which is incorporated herein by reference), the alkaline phosphatase promoter, a tryptophan (trp) promoter system (Goeddel, Nucleic Acids Res., 8: 4057 (1980), which is incorporated herein by reference), the PLtetO-1 and Plac/are-1 promoters (Lutz and Bujard, Nucleic Acids Res., 25: 1203-1210 (1997), which is incorporated herein by reference), and hybrid promoters such as the tac promoter (deBoer et al., Proc. Natl. Acad. Sci. USA, 80: 21-25 (1983), which is incorporated herein by reference).

In some embodiments, the heterologous nucleic acid described herein is operably linked to a promoter. In some embodiments, the promoter is a constitutive promoter. In some embodiments, the promoter is an inducible promoter. An inducible promoter useful in the methods and systems as disclosed herein can be induced by one or more physiological conditions, such as changes in pH, temperature, radiation, osmotic pressure, saline gradients, cell surface binding, and the concentration of one or more extrinsic or intrinsic inducing agents. The extrinsic inducer or inducing agent may comprise amino acids and amino acid analogs, saccharides and polysaccharides, nucleic acids, protein transcriptional activators and repressors, cytokines, toxins, petroleum-based compounds, metal containing compounds, salts, ions, enzyme substrate analogs, hormones, and combinations thereof. In specific embodiments, the inducible promoter is activated or repressed in response to a change of an environmental condition, such as the change in concentration of a chemical, metal, temperature, radiation, nutrient or change in pH. Thus, an inducible promoter useful in the methods and systems as disclosed herein can be a phage inducible promoter, nutrient inducible promoter, temperature inducible promoter, radiation inducible promoter, metal inducible promoter, hormone inducible promoter, steroid inducible promoter, and/or hybrids and combinations thereof. Appropriate environmental inducers can include, but are not limited to, exposure to heat (i.e., thermal pulses or constant heat exposure), various steroidal compounds, divalent cations (including Cu²⁺ and Zn²⁺), galactose, tetracycline, IPTG (isopropyl-β-D thiogalactoside), as well as other naturally occurring and synthetic inducing agents and gratuitous inducers.

Inducible promoters useful in the methods and systems as disclosed herein also include those that are repressed by “transcriptional repressors” that are subject to inactivation by the action of environmental, external agents, or the product of another gene. Such inducible promoters may also be termed “repressible promoters” where it is required to distinguish between other types of promoters in a given module or component of the biological switch converters described herein. Preferred repressors for use in the present invention are sensitive to inactivation by physiologically benign agent. Thus, where a lac repressor protein is used to control the expression of a promoter sequence that has been engineered to contain a lacO operator sequence, treatment of the host cell with IPTG will cause the dissociation of the lac repressor from the engineered promoter containing a lacO operator sequence and allow transcription to occur. Similarly, where a tet repressor is used to control the expression of a promoter sequence that has been engineered to contain a tetO operator sequence, treatment of the host cell with tetracycline will cause the dissociation of the tet repressor from the engineered promoter and allow transcription of the sequence downstream of the engineered promoter to occur.

A bacterial cell for use in the methods and compositions described herein can be any of any species. Preferably, the bacterial cells are of a species and/or strain which is amenable to culture and genetic manipulation. In some embodiments, the bacterial cell is a Gram-positive bacterial cell. In some embodiments, the bacterial cell is a Gram-negative bacterial cell. In some embodiments, the parental strain of the bacterial cell of the technology described herein can be a strain optimized for protein expression. Non-limiting examples of bacterial species and strains suitable for use in the present technologies include Escherichia coli, E. coli BL21, E. coli Tuner, E. coli Rosetta, E. coli JM101, and derivatives of any of the foregoing. Bacterial strains for protein expression are commercially available, e.g. EXPRESS™ Competent E. coli (Cat. No. C2523; New England Biosciences; Ipswich, Mass.). In some embodiments, the cell is an E. coli cell.

In some embodiments, the bacterium expresses wild-type CsgA. In some embodiments, the bacterium comprises a mutation and/or deletion in the wild-type CsgA gene, e.g., such that the cell does not express wild-type CsgA. In some embodiments, the heterologous nucleic acid described herein is introduced into a bacterial cell by homologous recombination, e.g., such that the heterologous nucleic acid replaces an endogenous csgA gene in the bacterial genome.

In one aspect, provided herein is a method for producing a recombinant protein (e.g., recombinant silk or collagen protein) comprising culturing an engineered bacterium described herein under conditions suitable for the expression of the recombinant protein in the engineered bacterium. In some embodiments, the recombinant protein is secreted from the engineered bacterium. In some embodiments, the methods comprise collecting the recombinant protein from the cell culture medium comprising the engineered bacterium or in which the engineered bacterium was cultured.

In some embodiments, the engineered bacterium is not exposed to a lysing agent prior to collecting the recombinant protein from the cell culture medium. In some embodiments, the recombinant polypeptide is collected from a supernatant of the cell culture medium. Methods for collecting a recombinant polypeptide from a cell culture medium are well known in the art, and include, for example, filtration, centrifugation, dialysis, crossflow filtration, ultrafiltration, acid precipitation, and lyophilization.

In some embodiments, the methods of producing a recombinant polypeptide described herein further comprise purifying the recombinant polypeptide. Recombinant polypeptides can also be isolated from cellular lysates and/or cell culture medium by using any standard technique known in the art. For example, recombinant polypeptides can be engineered to comprise an epitope tag such as a poly-histidine tag or other polypeptide tag such as myc or FLAG. Purification can be achieved by immunoprecipitation using antibodies specific to the recombinant peptide (or any epitope tag comprised in the amino sequence of the recombinant polypeptide) or by running the lysate solution or cell culture medium through an affinity column that comprises a matrix for the polypeptide or for any epitope tag comprised in the recombinant polypeptide (see for example, Ausubel et al., eds. (1993) Current Protocols in Molecular Biology, Section 10.11.8, John Wiley & Sons, New York).

Other methods for purifying a recombinant polypeptide include, but are not limited to ion exchange chromatography, hydroxylapatite chromatography, hydrophobic interaction chromatography, preparative isoelectric focusing chromatography, molecular sieve chromatography, HPLC, native gel electrophoresis in combination with gel elution, affinity chromatography, and preparative isoelectric. See, e.g., Marston et al. (1990) Meth. Enz., 182:264-275.

In another aspect, the present disclosure provides a recombinant protein (e.g., recombinant silk or collagen protein) as described herein. In some embodiments, the recombinant silk protein is produced using the methods described herein. In some embodiments, the recombinant protein comprises a periplasmic translocation signal sequence, an outer membrane signal sequence and a silk fibroin or collagen domain. In some embodiments, the recombinant protein comprises an outer membrane signal sequence and a silk fibroin or collagen domain. In some embodiments, the recombinant protein comprises an periplasmic translocation signal sequence and a silk fibroin or collagen domain. In some embodiments, the recombinant silk protein comprises a silk fibroin domain. In some embodiments, the recombinant collagen protein comprises a bacterial collagen domain. In some embodiments, the recombinant protein comprises a periplasmic translocation signal sequence, an outer membrane signal sequence, a silk fibroin or collagen domain, and one or more of an amyloid domain (e.g., CsgA), an elastin domain, and a collagen domain. In some embodiments, the recombinant protein comprises an outer membrane signal sequence, a silk fibroin or collagen domain, and one or more of an amyloid domain (e.g., CsgA), an elastin domain, and a collagen domain. In some embodiments, the recombinant protein comprises a periplasmic translocation signal sequence, a silk fibroin or collagen domain, and one or more of an amyloid domain (e.g., CsgA), an elastin domain, and a collagen domain. In some embodiments, the recombinant protein comprises a silk fibroin or collagen domain, and one or more of an amyloid domain (e.g., CsgA), an elastin domain, and a collagen domain. In some embodiments, the recombinant protein further comprises a functional protein selected from the group consisting of an enzyme, an antibody and a detectable protein. In some embodiments, the detectable protein is selected from the group consisting of poly-histidine tag, a myc tag, a FLAG tag, a hemagglutinin (HA) tag, and a V5 tag. In some embodiments, the recombinant polypeptide comprises a protease cleavage site amino acid sequence.

In another aspect, provided herein is a curli fiber comprising a plurality of recombinant proteins as described herein. In some embodiments, the curli fiber comprises a plurality of recombinant silk proteins, wherein the plurality of silk proteins comprise a silk fibroin domain and an amyloid domain. In some embodiments, the curli fiber comprises a plurality of recombinant collagen proteins, wherein the plurality of collagen proteins comprise a bacterial collagen domain (e.g., a CL domain) and an amyloid domain. In some embodiments, the curli fiber comprises a plurality of recombinant proteins disclosed herein, wherein the plurality of proteins comprise a periplasmic translocation signal sequence, an outer membrane signal sequence, a silk fibroin or collagen domain, an amyloid domain (e.g., CsgA), and optionally, one or more of an elastin domain, and a collagen domain. In some embodiments, the curli fiber comprises a plurality of recombinant silk proteins, wherein the plurality of silk proteins comprise an outer membrane signal sequence, a silk fibroin domain, an amyloid domain (e.g., CsgA), and optionally, one or more of an elastin domain, and a collagen domain. In some embodiments, the curli fiber comprises a plurality of recombinant silk proteins, wherein the plurality of silk proteins comprise a periplasmic translocation signal sequence, a silk fibroin domain, an amyloid domain (e.g., CsgA), and optionally, one or more of an elastin domain, and a collagen domain. In some embodiments, the curli fiber comprises a plurality of recombinant silk proteins, wherein the plurality of silk proteins comprise a silk fibroin domain, an amyloid domain (e.g., CsgA), and optionally, one or more of an elastin domain, and a collagen domain. In some embodiments, the curli fiber comprises a plurality of recombinant silk proteins, wherein the plurality of silk proteins further comprises a functional protein selected from the group consisting of an enzyme, an antibody and a detectable protein. In some embodiments, the detectable protein is selected from the group consisting of poly-histidine tag, a myc tag, a FLAG tag, a hemagglutinin (HA) tag, and a V5 tag. In some embodiments, the curli fiber comprises a plurality of recombinant silk proteins, wherein the plurality of silk proteins comprise a protease cleavage site amino acid sequence.

In one aspect, provided herein is a biofilm comprising an engineered bacterium described herein, e.g., an engineered bacterium comprising a heterologous nucleic acid encoding a recombinant protein, wherein the recombinant protein comprises a periplasmic translocation signal sequence, an outer membrane secretion signal sequence, and a silk fibroin or collagen domain. In another aspect, provided herein is a biofilm comprising a cell comprising one or more engineered CsgA polypeptide and/or comprising a vector or nucleic acid encoding such a polypeptide.

In another aspect, provided herein is a biofilm comprising a curli fiber formed from a plurality of recombinant silk proteins as described herein. In some embodiments, the biofilm comprises a curli fiber formed from a plurality of recombinant silk proteins, wherein the recombinant silk proteins comprise a silk fibroin domain and an amyloid domain.

In another aspect, provided herein are biofilms, hydrogels and triple-helical fiber meshworks comprising a plurality of recombinant collagen proteins as described herein. In some embodiments, the biofilms, hydrogels and triple-helical fiber meshworks comprise a collagen fiber formed from a plurality of recombinant collagen proteins (e.g., CL domain peptides), wherein the recombinant collagen proteins form a stable triple helix capable of elongation and bundling. Such collagen-based structures as are disclosed herein may include physical or chemical modification of the collagen to improve stability, such as by physical or chemical modification. Such crosslinkers are known in the art and include genipen and the like

As used herein, a “biofilm” refers to a mass of microorganisms or extracellular proteins which can adhere or is adhering to a surface. A biofilm comprises a matrix of extracellular polymeric substances, including, but not limited to extracellular DNA, proteins, glycopeptides, and polysaccharides. For example, and without limitation, biofilms may be formed from the isolated and/or purified recombinant collagen disclosed herein. The nature of a biofilm, such as its structure and composition, can depend on the particular proteins and/or species of bacteria present in the biofilm. Bacteria present in a biofilm are commonly genetically or phenotypically different than corresponding bacteria not in a biofilm, such as isolated bacteria or bacteria in a colony.

In some embodiments, the technology described herein relates to a biofilm that is produced by culturing an engineered bacterium described herein under conditions suitable for the production of a biofilm. Conditions suitable for the production of a biofilm can include, but are not limited to, conditions under which the microbial cell is capable of logarithmic growth and/or polypeptide synthesis. Conditions may vary depending upon the species and strain of microbial cell selected. Conditions for the culture of microbial cells are well known in the art. Biofilm production can also be induced and/or enhanced by methods well known in the art, e.g. contacting cells with subinhibitory concentrations of beta-lactam or aminoglycoside antibiotics, exposing cells to fluid flow, contacting cells with exogenous poly-N-acetylglucosamine (PNAG), or contacting cells with quorum sensing signal molecules. In some embodiments, conditions suitable for the production of a biofilm can also include conditions which increase the expression and secretion of CsgA, e.g., by exogenously expressing CsgD. In some embodiments, the biofilm can comprise the bacterium which produced the biofilm. In some embodiments, described herein is a composition comprising an engineered CsgA polypeptide which includes CsgA attached to a polypeptide such as spider silk or collagen, as described herein.

When expressed by a bacterium capable of forming curli, e.g. a bacterium expressing CsgA, CsgB, CsgC, CsgD, CsgE, CsgF, and CsgG or some subset thereof, CsgA units will be assembled to form curli filaments, e.g., polymeric chains of CsgA or of a recombinant silk protein comprising an amyloid domain as described herein. In some embodiments, filaments of the polypeptide can be present in the composition. In some embodiments, the filaments can be part of a proteinaceous network, e.g., multiple filaments which can be, e.g., interwoven, overlapping, and/or in contact with each other. In some embodiments, the proteinaceous network can comprise additional biofilm components, e.g., materials typically found in an E. coli biofilm. Non-limiting examples of biofilm components can include biofilm proteins (e.g. FimA, FimH, Ag43, AidA, and/or TibA) and/or non-proteinaceous biofilm components (e.g. cellulose, PGA and/or colonic acid). In some embodiments, the composition can further comprise a cell comprising an engineered CsgA polypeptide and/or comprising a vector or nucleic acid encoding such a polypeptide.

Definitions of common terms in cell biology and molecular biology can be found in The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); Benjamin Lewin, Genes X, published by Jones & Bartlett Publishing, 2009 (ISBN-10: 0763766321); Kendrew et al. (eds.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8) and Current Protocols in Protein Sciences 2009, Wiley Intersciences, Coligan et al., eds.

Unless otherwise stated, the present invention was performed using standard procedures, as described, for example in Sambrook et al., Molecular Cloning: A Laboratory Manual (3 ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2001); Davis et al., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (1995); or Methods in Enzymology: Guide to Molecular Cloning Techniques Vol. 152, S. L. Berger and A. R. Kimmel Eds., Academic Press Inc., San Diego, USA (1987); and Current Protocols in Protein Science (CPPS) (John E. Coligan, et. al., ed., John Wiley and Sons, Inc.), which are all incorporated by reference herein in their entireties.

The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments may perform functions in a different order, or functions may be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. Moreover, due to biological functional equivalency considerations, some changes can be made in protein structure without affecting the biological or chemical action in kind or amount. These and other changes can be made to the disclosure in light of the detailed description. All such modifications are intended to be included within the scope of the appended claims.

Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.

The following examples are set forth as being representative of the present disclosure. These examples are not to be construed as limiting the scope of the present disclosure as these and other equivalent embodiments will be apparent in view of the present disclosure, figures and accompanying claims.

Example I: Genetic Construction of Silk Gene Constructs

Protein motifs of dragline silk from Nephila clavipes (Golden Silk Orb-weaving spider) were synthetically synthesized and concatenated using molecular biology techniques to create silk domains and amyloid-silk domain fusions that are secreted through the T8SS functional amyloid secretion pathway of E. coli. Additional consensus dragline silk sequences are set forth in SEQ ID NOS: 2054-2074.

Spider silk from the Golden Silk Orb-weaving spider Nephila clavipes has been extensively studied for its mechanical properties. The major protein constituent of dragline silk from N. clavipes is the major ampullate spidroin-1 (MaSp1). The repetitive domain of the silks is a repeated protein motif that influences its resulting mechanical properties. As depicted in FIGS. 3A and 3B, the repetitive 35-amino acid peptide motif was used as the ‘silk domain’ in the constructs, which were synthetized and engineered into fusion proteins containing 4, 8, 16, 32, and 64 head-to-tail repeating domains, ranging in size from 17-202 amino acids. To test the ability of these constructs to be secreted from the cells via the T8SS pathway, a N-terminal tag was added consisting of the CsgA signal sequence, consisting of a 20-amino acid Sec sequence for periplasmic localization and a 22-amino acid N22 domain which directs the protein to the CsgG/CsgE outer membrane complex for secretion. A second set of fusion constructs with the full CsgA protein located N-terminal to the silk domain, resulting in bifunctional self-assembling silks, was also tested for secretion. See FIG. 2.

More specifically, and with reference to FIG. 6, the gene for the major ampullate spidroin 1 spider silk protein from Nephila clavipes was computationally codon optimized for Escherichia coli expression from the know protein sequence (see Xu, M., & Lewis, R. V. (1990) Structure of a protein superfiber: spider dragline silk. Proc. Natl. Acad. Sci. USA, 87(18), 7120-7124, hereby incorporated by reference in its entirety.

Using this optimized gene sequence, a 4-mer containing four consecutive repeats of the spider silk domain was ordered as a synthetic DNA construct with flanking restriction sites which allowed head-to-tail concatenation through molecular biology cloning to generate longer proteins with repeating spider silk domains. This is advantageous as the molecular weight of the spider silk proteins directly correlates with the physical properties of the spider silk. See Xia, X.-X., Qian, Z.-G., Ki, C. S., Park, Y. H., Kaplan, D. L., & Lee, S. Y. (2010). Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber. Proc. Natl. Acad. Sci. USA 107(32), 14059-14063, hereby incorporated by reference in its entirety.

The 4-mer repeat, herein referred to as Silk4, was created with an N-terminal NheI restriction site. Immediately following the Silk4 domain, the construct was engineered with a multiple cloning site consisting of SpeI-KpnI-BamHI, a 6x-histidine tag, and finally, a stop codon. The final plasmid was inserted into pET30a-ACEFG plasmid, which contains 5 genes of the wildtype curli operon, csgA, csgC, csgE, csgF, and csgG. For the spider silk only constructs, the Silk4 construct was inserted in place of the CsgA curlin domains, resulting in a Sec-N22 tagged Silk4 construct. For the spider silk-CsgA fusions, the Silk4 construct was cloned behind the csgA gene to create a fusion protein containing the native CsgA protein, a -GSGGSG- linker, and the Silk4 construct.

To generate expression constructs containing various amounts of spider silk domains, the designed restriction sites were used in a concatenation strategy to generate Silk8 (8 consecutive domains), Silk16 (16 consecutive domains), Silk32 (32 consecutive domains), and Silk64 (64 consecutive domains). Briefly, the Silk4 constructs were digested by NheI and BamHI and the Silk4 dropout was isolated. Also, the Silk4 constructs were digested by SpeI and BamHI and the major linearized plasmid was isolated. The dropout was ligated into the digested plasmid. Since NheI and SpeI have compatible overhangs, they combine to generate a “scar” in which two concatenated Silk4 domains are linked by nucleotides encoding for an -AS- linker. This resulting plasmid, containing 8 total spider silk domains, was named Silk8. The remaining signal sequence only and CsgA fusion constructs were cloned in a similar manner.

Example II: Expression of Spider Silk Domains Using the CsgA (Sec-N22) Signal Sequence

For the experiments shown herein, the Rosetta-gami 2(DE3) cell lines from Novagen, which are pET vector compatible, were used. The constructs here could also be cloned into other plasmid systems and other E. coli strains. To test the transformed cells for spider silk expression, LB plates were made with the proper plasmid selectable marker and supplemented with 30 μg/mL of Congo red dye and 0.05 mM IPTG. Congo red has been shown to bind to silk, and any extracellularly produced silk will bind to the dye. See Slotta, U., Hess, S., Spieß, K., Stromer, T., Serpell, L., & Scheibel, T. (2007). Spider Silk and Amyloid Fibrils: A Structural Comparison. Macromolecular Bioscience, 7(2), 183-188, hereby incorporated by reference in its entirety.

All transformants were grown in LB media with antibiotic and 0.5% glucose overnight at room temperature, pelleted, and then resuspended in LB to an OD600 of 0.5. This culture was then spotted onto the LB-Congo red agar plates, allowed to dry, and then incubated at 25° C. for 48 hours before imaging.

Spider silk domain repeats were cloned in front of the CsgA signal sequence, which includes a Sec translocation sequence for periplasmic localization and the N22 sequence, which is a CsgG-specific signal for transport through the outer membrane. The transformants were grown and spotted onto LB plates containing Congo red, a red dye which has been shown to bind to silk, as illustrated in FIG. 4. See dos Santos-Pinto, J. R. A. et al. Structural Model for the Spider Silk Protein Spidroin-1. J. Proteome Res. 150811080734002 (2015) hereby incorporated by reference in its entirety. Since these silk domains are not tethered to the cell surface, one would expect to see a red halo around the spotted cells as the silk proteins diffuse through the agar and bind to the dye, especially for constructs of a lower molecular weight. This was observed for SS-Silk4 and, to a lesser extent, the SS-Silk8 spots. As depicted in FIG. 3A, Sec-N22-[Silk]_(N)-HisTag constructs are secreted by the E. coli T8SS pathway. SS-Silk constructs transformed into E. coli and plated onto Congo Red LB plates and induced with 0.05 mM IPTG. The negative control plasmid encodes for a non-CR binding protein, BSA. See FIGS. 3A and 3B. Various Sec-N22 secretion tag constructs were tested, as shown in Table 1. Various Sec-N22 amyloid-silk fusion constructs were tested, as shown in Table 2.

TABLE 1 SEC-N22 SECRETION TAG SILK CONSTRUCTS GENE SIZE PROTEIN SIZE MOLECULAR CONSTRUCT (BP) (RESIDUES) WEIGHT (_(K)D_(A)) SS-Silk4 474 198 17.29 SS-Silk8 900 339 28.91 SS-Silk16 1752 621 52.14 SS-Silk32 3456 1185 98.61 SS-Silk64 6864 2313 191.55

TABLE 2 SEC-N22 AMYLOID-SILK FUSION CONSTRUCTS GENE SIZE PROTEIN SIZE MOLECULAR CONSTRUCT (BP) (RESIDUES) WEIGHT (_(K)D_(A)) SS-Silk4 474 198 17.29 SS-Silk8 900 339 28.91 SS-Silk16 1752 621 52.14 SS-Silk32 3456 1185 98.61 SS-Silk64 6864 2313 191.55

Example III: Expression of Spider Silk Domains as a Fusion to the CsgA Protein

To determine if silk-protein fused to different functional proteins could be secreted to generate a programmable silk material, CsgA-silk domain fusions were tested. As depicted in FIG. 3B, these constructs also contain the Sec-N22 T8SS secretion signal domains. These CsgA-silk fusions would assemble extracellularly into a hybrid amyloid-silk material. See FIG. 2. These constructs, when expressed in E. coli and spotted onto LB-CR plates, show clear Congo Red binding, indicating successful secretion of these silk-protein fusions. See FIG. 5.

FIG. 3B depicts the Sec-N22-CsgA-[Silk]_(N)-HisTag constructs secreted by the E. coli T8SS pathway. The fusion proteins were transformed into E. coli and plated onto Congo Red LB plates and induced with 0.05 mM IPTG. The negative control plasmid encodes for a non-CR binding protein, BSA. See FIGS. 3A and 3B.

Example IV: Additional Applications

Aspects of the present disclosure utilize the modified bacterial cells which express a silk protein or a CsgA-silk fusion. Silks have been intensely researched for its potential use in a plethora of different applications. As it can be assembled into different forms (fibers, thin films, foams, etc.) the applications are likewise varied. Methods described herein decrease processing costs for silk proteins. A small sampling of the commercial applications for silk proteins products are listed in the table below. In addition, other anticipated applications of the disclosed production process may include: use in a manufacturing process for the production of various silk proteins for use in high performance textiles (e.g., sporting wear, protective armor, etc.), hydrogels, films, or foams, or biomedical devices. Use in combination with optimized curli secretion systems in other engineered strains of E. coli. In vivo production of silk-based materials (e.g., in the GI tract) for therapeutic or diagnostic purposes. Production of silk-based materials in agricultural settings, such as on the surface of leaves, plants, roots, or in soil. Uses are shown in Table 3.

TABLE 3 APPLICATIONS TYPE OF FABRICATION MARKET APPLICATION Fibers Industrial Super-tough fabrics and composites^(6,18) Fibers Industrial Large-scale 3D printed structures¹ Fibers Biomedical Functionalized superior sutures and medical bandages^(20,21) Fibers Biomedical Artificial biomimetic muscles²² Foams Biomedical Biomaterials for tissue bioengineering scaffolds^(23,24) Foams Biomedical Injectable tetrahertz waveguides²⁵ Thin Films Industrial Transparent photonic films²⁶ Thin Films Industrial/ Biocompatible flexible electrodes²⁷ Biomedical Thin Films Biomedical Brain electrode coatings²⁸ Thin Films Biomedical Drug storage and delivery²⁹ Thin Films Biomedical Vaccine stabilization³⁰ Thin Films Biomedical Antibiotic stabilization³⁰ Thin Films Biomedical Virus stabilization³¹ Thin Films Biomedical Enzyme stabilization³² Films Industrial/ Microfluidic devices³³ Biomedical Particles/Spheres Biomedical Drug storage and de1ivery³⁴⁻³⁶ Particles/Spheres Industrial Battery energy storage materials³⁶

REFERENCES

Each of the following references is hereby incorporated by reference in its entirety.

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Molecular and nanostructural mechanisms of deformation, strength and     toughness of spider silk fibrils. Nano Lett. 10, 2626-34 (2010). -   13. Chapman, M. R. et al. Role of Escherichia coli curli operons in     directing amyloid fiber formation. Science 295, 851-855 (2002). -   14. Desvaux, M., Hébraud, M., Talon, R. & Henderson, I. R. Secretion     and subcellular localizations of bacterial proteins: a semantic     awareness issue. Trends Microbiol. 17, 139-45 (2009). -   15. Sivanathan, V. & Hochschild, A. Generating extracellular amyloid     aggregates using E. coli cells. Genes Dev. 26, 2659-2667 (2012). -   16. Widmaier, D. M. & Voigt, C. a. Quantification of the     physiochemical constraints on the export of spider silk proteins by     Salmonella type III secretion. Microb. Cell Fact. 9, 78 (2010). -   17. dos Santos-Pinto, J. R. A. et al. Structural Model for the     Spider Silk Protein Spidroin-1. J. Proteome Res. 150811080734002     (2015). doi:10.1021/acs.jproteome.5b00243. -   18. Heidebrecht, A. et al. Biomimetic Fibers Made of Recombinant     Spidroins with the Same Toughness as Natural Spider Silk. Adv.     Mater. 4, 1-6 (2015). -   19. Schacht, K. et al. Biofabrication of cell-loaded 3D spider silk     constructs. Angew. Chem. Int. Ed. Engl. 54, 2816-20 (2015). -   20. Chen, X. et al. Antibacterial Surgical Silk Sutures Using a     High-Performance Slow-Release Carrier Coating System. ACS Appl.     Mater. Interfaces 7, 22394-403 (2015). -   21. Calamak, S., Erdo{hacek over (g)}du, C., Ozalp, M. &     Ulubayram, K. Silk fibroin based antibacterial bionanotextiles as     wound dressing materials. Mater. Sci. Eng. C. Mater. Biol. Appl. 43,     11-20 (2014). -   22. Agnarsson, I., Dhinojwala, A., Sahni, V. & Blackledge, T. a.     Spider silk as a novel high performance biomimetic muscle driven by     humidity. J. Exp. Biol. 212, 1990-1994 (2009). -   23. Wang, S., Ghezzi, C. E., White, J. D. & Kaplan, D. L. Coculture     of dorsal root ganglion neurons and differentiated human corneal     stromal stem cells on silk-based scaffolds. J. Biomed. Mater. Res. A     103, 3339-48 (2015). -   24. Yao, D., Liu, H. & Fan, Y. Silk scaffolds for musculoskeletal     tissue engineering. Exp. Biol. Med. (Maywood). (2015).     doi:10.1177/1535370215606994. -   25. Guerboukha, H., Yan, G., Skorobogata, O. & Skorobogatiy, M. Silk     Foam Terahertz Waveguides. Adv. Opt. Mater. n/a-n/a (2014).     doi:10.1002/adom.201400228. -   26. Perry, H., Gopinath, A., Kaplan, D. L., Negro, L. D. &     Omenetto, F. G. Nano- and micropatterning of optically transparent,     mechanically robust, biocompatible silk fibroin films. Adv. Mater.     20, 3070-3072 (2008). -   27. Kim, D.-H. et al. Dissolvable films of silk fibroin for     ultrathin conformal bio-integrated electronics. Nat. Mater. 9, 511-7     (2010). -   28. Tien, L. W. et al. Silk as a multifunctional biomaterial     substrate for reduced glial scarring around brain-penetrating     electrodes. Adv. Funct. Mater. 23, 3185-3193 (2013). -   29. Yucel, T., Lovett, M. L. & Kaplan, D. L. Silk-based biomaterials     for sustained drug delivery. J. Control. Release 190, 381-97 (2014). -   30. Zhang, J. et al. Stabilization of vaccines and antibiotics in     silk and eliminating the cold chain. Proc. Natl. Acad. Sci. U.S.A.     109, 11981-6 (2012). -   31. Sutherland, T. D. et al. Stabilization of viruses by     encapsulation in silk proteins. ACS Appl. Mater. Interfaces 6,     18189-96 (2014). -   32. Lu, Q. et al. Stabilization and release of enzymes from silk     films. Macromol. Biosci. 10, 359-68 (2010). -   33. Bettinger, C. J. et al. Silk Fibroin Microfluidic Devices. Adv.     Mater. 19, 2847-2850 (2007). -   34. Tian, Y., Jiang, X., Chen, X., Shao, Z. & Yang, W.     Doxorubicin-loaded magnetic silk fibroin nanoparticles for targeted     therapy of multidrug-resistant cancer. Adv. Mater. 26, 7393-8     (2014). -   35. Qu, J. et al. Silk fibroin nanoparticles prepared by     electrospray as controlled release carriers of cisplatin. Mater.     Sci. Eng. C. Mater. Biol. Appl. 44, 166-74 (2014). -   36. Sheng, W. et al. Silk-regulated hierarchical hollow     magnetite/carbon nanocomposite spheroids for lithium-ion battery     anodes. Nanotechnology 26, 115603 (2015).

Example V Materials and Methods for Collagen Expression and Assessment Cell Strains, Plasmids, and Collagen Expression

The pET21d-csgACEFG plasmid and the curli operon deletion mutant strain of E. coli, PQN4. The pET21d plasmid was used with the curli operon (without the CsgB nucleator protein) under the control of the T7 promoter, as template vector to synthesize the bacterial collagen. On this template vector, the encoding genes that are necessary for extracellular secretion of the bacterial collagen were genetically added and eliminated the csgA that encodes the major subunit of the curli fibers, CsgA, and replaced it with a gene coding for bacterial collagen. The pET21d-csgACEFG plasmid was linearized using forward and reverse primers starting at immediately downstream and immediately upstream, respectively, to remove the csgA gene. Then, the collagen DNA fragment (Life technologies) was inserted downstream of N22 using isothermal Gibson assembly reaction (New England Biolabs). Also, a translational enhancing element (TEE) encoding the amino acids MNHKVHM (SEQ ID NO: 2086) was added at N-terminus of the collagen sequence, which has been shown to enhance translation initiation. Qing, G. et al. Cold-shock induced high-yield protein production in Escherichia coli. Nat Biotechnol 22, 877-882, (2004). The TEE was followed by a six-histidine tag (His-tag) to allow for immunodetection. The templated vector for the secretion system, which consists of the genes expressing SEC, N22, His-tag, and collagen, and the curli-specific genes (csg), csgC, csgE, csgF, and csgG (pET21d-v′cl-csgCEFG) was transformed into E. coli PQN4 and BL21(DE3) (New Englan Biolabs). FIG. 8A demonstrates the arrangement of the encoding genes on the template vector. To express the proteins, the transformed PQN4 cells were streaked onto lysogeny broth (LB) agar plates containing 100 μg/mL carbenicillin and 0.5% (m/v) glucose (for catabolite repression of T7 RNA polymerase). Colonies were picked from the plates, and 5 mL cultures were inoculated (in LB containing and 100 μg/mL carbenicillin and 2% (m/v) glucose). Cultures were grown overnight at 37° C. with an agitation rate of 250 rpm. The overnight cultures were diluted 100-fold in fresh LB medium with 100 μg/mL carbenicillin and protein expression was allowed to proceed at 37° C. overnight.

The protein sequence of the bacterial collagen and DNA sequences of all the genes and primers are listed in the Table 4. The nucleotide sequence of the assembled plasmid, includes the expressed insertion.

TABLE 4 Protein sequence of the bacterial collagen and DNA sequences of the genes involved for extracellular secretion of bacterial collagen Protein sequence of the DEQEEKAKVRTEFIQELAQGLGGIEKKNFPTLGDEDLDHTYMTKLLTYLQE variable domain (V′) REQAENSWRKRLLKGIQDHALDLVPRGSP (SEQ ID NO: 2075) Protein sequence of GQDGRNGERGEQGPTGPTGPAGPRGLQGLQGLQGERGEQGPTGPAGPRGL bacterial collagen (CL) QGERGEQGPTGLAGKAGEAGAKGETGPAGPQGPRGEQGPQGLPGKDGEA GAQGPAGPMGPAGERGEKGEPGTQGAKGDRGETGPVGPRGERGEAGPAG KDGERGPVGPAGKDGQNGQDGLPGKDGKDGQNGKDGLPGKDGKDGQN GKDGLPGKDGKDGQDGKDGLPGKDGKDGLPGKDGKDGQPGKP (SEQ ID NO: 2076) Forward primer TCTGAGCTGAACATTTACCAGTACGG (SEQ ID NO: 2077) Reverse primer ATTTGGGCCGCTATTATTACCGCC (SEQ ID NO: 2078) SEC ATGAAACTTTTAAAAGTAGCAGCAATTGCAGCAATCGTATTCTCCGGTA GCGCTCTGGCA (SEQ ID NO: 2079) N22 GGTGTTGTTCCTCAGTACGGCGGCGGCGGTAACCACGGTGGTGGCGGT AATAATAGCGGCCCAAAT (SEQ ID NO: 2080) Translational ATGAACCATAAGGTTCAC (SEQ ID NO: 2081) enhancing element (TEE) CsgC ATGAATACGTTATTACTCCTTGCGGCACTTTCCAGTCAGATAACCTTTA ATACGACCCAGCAAGGGGATGTGTATACCATTATTCCTGAAGTCACTCT TACTCAATCTTGTCTGTGCAGAGTACAAATATTGTCCCTGCGCGAAGGC AGTTCAGGGCAAAGTCAGACGAAGCAAGAAAAGACCCTTTCATTGCCT GCTAATCAACCCATTGCTTTGACGAAGTTGAGTTTAAATATTTCCCCGG ACGATCGGGTGAAAATAGTTGTTACTGTTTCTGATGGACAGTCACTTCA TTTATCACAACAATGGCCGCCCTCTTCAGAAAAGTCTTAA (SEQ ID NO: 2082) CsgE ATGAAACGTTAtttACGCTGGATTGTGGCGGCAGAATTTCTGTTCGCCGC AGGGAATCTTCACGCCGTTGAGGTAGAAGTCCCGGGATTGCTAACTGA CCATACTGTTTCATCTATTGGCCATGATTTTTACCGAGCCTTTAGTGATA AATGGGAAAGTGACTATACGGGTAACTTAACGATTAATGAAAGGCCCA GTGCACGATGGGGAAGCTGGATCACTATAACGGTCAATCAGGACGTTA TTTTCCAGACTTTTTTATTTCCGTTGAAAAGAGACTTCGAGAAAACTGT CGTCTTTGCACTGATTCAAACTGAAGAAGCACTAAATCGTCGCCAGATA AATCAGGCGTTATTAAGTACGGGCGATTTGGCGCATGATGAATTCTAA (SEQ ID NO: 2083) CsgF ATGCGTGTCAAACATGCAGTAGTTCTACTCATGCTTATTTCGCCATTAA GTTGGGCTGGAACCATGACTTTCCAGTTCCGTAATCCAAACTTTGGTGG TAACCCAAATAATGGCGCTTTTTTATTAAATAGCGCTCAGGCCCAAAAC TCTTATAAAGATCCGAGCTATAACGATGACTTTGGTATTGAAACACCCT CAGCGTTAGATAACTTTACTCAGGCCATCCAGTCACAAATTTTAGGTGG GCTACTGTCGAATATTAATACCGGTAAACCGGGCCGCATGGTGACCAA CGATTATATTGTCGATATTGCCAACCGCGATGGTCAATTGCAGTTGAAC GTGACAGATCGTAAAACCGGACAAACCTCGACCAtCCAGGTTTCGGGTT TACAAAATAACTCAACCGATTTTTAA (SEQ ID NO: 2084) CsgG ATGCAGCGCTTATTTCTTTTGGTTGCCGTCATGTTACTGAGCGGATGCTT AACCGCCCCGCCTAAAGAAGCCGCCAGACCGACATTAATGCCTCGTGC TCAGAGCTACAAAGATTTGACCCATCTGCCAGCGCCGACGGGTAAAAT CTTTGTTTCGGTATACAACATTCAGGACGAAACCGGGCAATTTAAACCC TACCCGGCAAGTAACTTCTCCACTGCTGTTCCGCAAAGCGCCACGGCAA TGCTGGTCACGGCACTGAAAGATTCTCGCTGGTTTATACCGCTGGAGCG CCAGGGCTTACAAAACCTGCTTAACGAGCGCAAGATTATTCGTGCGGC ACAAGAAAACGGCACGGTTGCCATTAATAACCGAATCCCGCTGCAATC TTTAACGGCGGCAAATATCATGGTTGAAGGTTCGATTATCGGTTATGAA AGCAACGTCAAATCTGGCGGGGTTGGGGCAAGATATTTTGGCATCGGT GCCGACACGCAATACCAGCTCGATCAGATTGCCGTGAACCTGCGCGTC GTCAATGTGAGTACCGGCGAGATCCTTTCTTCGGTGAACACCAGTAAGA CGATACTTTCCTATGAAGTTCAGGCCGGGGTTTTCCGCTTTATTGACTAC CAGCGCTTGCTTGAAGGGGAAGTGGGTTACACCTCGAACGAACCTGTT ATGCTGTGCCTGATGTCGGCTATCGAAACAGGGGTCATTTTCCTGATTA ATGATGGTATCGACCGTGGTCTGTGGGATTTGCAAAATAAAGCAGAAC GGCAGAATGACATTCTGGTGAAATACCGCCATATGTCGGTTCCACCGG AATCCTGA (SEQ ID NO: 2085)

Assessment of Collagen Expression, Purity, and Secretion by SDS-PAGE and Western Blotting.

The expression of his-tagged collagen and its secretion into the culture medium was confirmed by running a SDS-PAGE gel of different fractions of the culture and detecting collagen via Western blot. Three samples were used; 30 uL sample taken from a 5 mL freshly expressed culture, supernatant (30 uL), and washed bacterial pellets. To prepare the pellets, 1 mL of the culture was centrifuged, the supernatant removed, and after 1 wash with HCl 0.05 M and two washes with water, they were resuspended with 1 mL water. All samples were run on a NuPAGE Novex 4-12% Bis-Tris gel and transferred on an iBlot PVDF membrane (Invitrogen). The membrane was treated with a monoclonal mouse anti-His antibody, the HRP conjugate (Abcam), after blocking with 10% milk in TBST HRP. The chemiluminescence was detected using a FluorChem M system (Protein Simple) and the collagen was relatively quantified in the different fractions with ImageJ. The same samples were also loaded on TGX gel and stained with Coomassie Blue for more assessing along with the western blot results. SDS-PAGE was used to assess the purity of the purified collagen samples and confirm their molecular weights. After re-suspending the 30 uL of the purified collagen solution (5 mg/mL) in 10 uL 4× Laemmli loading buffer, it was loaded in each 50 μL-wells of a pre-cast Mini-Protean TGX gel (Bio-Rad Laboratories). The gels were electrophoresed at 200 V for 30 minutes and then stained with Coomassie Blue.

Assessment of Collagen Expression, Secretion, and Folding by Sirius Red Staining.

The supernatant of a collagen expressing culture was stained with Sirius Red and Masson's Trichrome and was compared with the supernatant of a non-transformed PQN4 culture, as control. For Sirius Red staining, ˜10 μL of the supernatant were air-dried on a glass slide for 5-10 min and were heat fixed by gently passing the slides over a flame. The slides were immersed for 1 h in saturated picric acid containing 0.1% Direct Red 80 (i.e., Sirius Red, Sigma) and washed by 0.5% acetic acid (2 times for 2 min). The slides were dehydrated by increasing concentrations of absolute alcohol (95%, 100%, 100%) each for 2 min followed by a xylene wash, and mounted in Neo-Mount resin (VWR). Birefringence images of the stained samples were taken using a polarized light microscope (Axio Scope.A1, Zeiss) equipped with a 6-megapixel CCD camera (Axiocam 505 color, Zeiss). Rat tail collagen (Sigma-Aldrich) was used as control for type I animal collagen.

For Masson's Trichrome (Sigma Aldrich) staining, the manufacturer's protocol was followed. Briefly, the samples were stained for 5 min stepwise in separate solutions of Weigert's Iron Hematoxylin, Biebrich Scarlet-Acid Fuchsin, phosphomolybdic-phosphotungstic acid, and aniline blue. The same steps as Sirius Red staining were followed for washing, dehydrating, mounting, and imaging.

Purification of Collagen Proteins Using Ni-NTA Column.

A Ni-NTA column for collagen purification was used as the gold-standard method. The collected supernatant was first filtered through 0.2 μm bottle filters (Thermo Fisher) to remove the large particulates and possible remained bacteria. The Ni-NTA column was incubated with the supernatant for 2 hours, washed with 40 mM imidazole solution 5 times to remove the non-specifically bound proteins, and washed with 500 mM imidazole solution to elute the bound proteins. Then, the eluate was concentrated and washed with a 30 kDa PALL centrifugal filter. To remove the non-collagen domain (V′), the purified protein was adjusted to pH=2.2 with HCl and incubated with trypsin (0.01 mg/mL) for 24 hours at 4° C. To stop the digestion, the pH was adjusted with 0.1 N NaOH to pH 8.0 and the protein solution was washed through 10 kDa PALL centrifugal filter.

Isolation of Collagen Proteins Using Digestion/Cross-Flow Filtration.

The supernatant was collected by 30 min centrifugation at 4000×g. After filtering the supernatant through 0.2 μm bottle filters, the pH was lowered to 2 (optimum pH for pepsin function (Johnston, N., Dettmar, P. W., Bishwokarma, B., Lively, M. O. & Koufman, J. A. Activity/stability of human pepsin: implications for reflux attributed laryngeal disease. Laryngoscope 117, 1036-1039, (2007)), pepsin was added to the supernatant at a final concentration of 0.01 mg/mL, and incubated at 4° C. for overnight for pepsin to digest the pepsin-sensitive impurities. Next, the voluminous crude protein solution was concentrated by crossflow filtration. A Minimate™ tangential flow filtration system (Pall Life Sciences) was used to filter 500 mL of digested supernatant through a 10 kDa molecular weight cut-off (MWCO) membrane. The permeate containing small solutes and digested proteins was discarded, and the concentrated retentate (containing collagen) was collected as product (FIG. 10A). The retentate was further washed with 500 mL of 10 mM sodium phosphate buffer.

Isolation of Collagen Proteins Using Digestion/Precipitation.

Another approach used to concentrate the large volume of the digested supernatant was acid precipitation. Phosphotungstic acid (PTA) was used at a final concentration of % 0.1, to precipitate the digested and non-digested proteins (collagen) from 100 mL supernatant. To prevent the denaturation of the collagen structure during acid precipitation, erythritol (0.5 M) was added to the protein solution and incubated on ice for 2 min (FIG. 10A). After collecting the precipitated proteins by centrifugation at 4000×g for 5 min, the precipitates were washed with 5 mL acetone 2 times and air-dried them for 30 min. Then, the precipitate was resolubilized in 10 mL NaOH (0.05 N) and washed with a 10 kDa centrifugal filter (Pall) to remove remaining small-size digested impurities from the final product. After the isolation process, the collected purified collagen solution (1 mL) was further washed with 10 mM sodium phosphate buffer pH=7.4 with the centrifugal filter and lyophilized.

Electron Microscopy and Nanostructure of Collagen Fibril.

Samples for scanning electron microscopy (SEM) were prepared by depositing 50 uL of the freshly expressed bacterial culture on 0.2 μm polycarbonate filter membranes (Whatman® Nuclepore from Millipore Sigma). The membranes were washed with 0.1 M sodium cacodylate buffer (Electron Microscopy Sciences), fixed with 2% (v/v) glutaraldehyde (Bio Basic) and 2% (v/v) paraformaldehyde (Electron Microscopy Sciences) for 2 hours at room temperature, and solvent-exchanged sequentially in 0%, 25%, 50%, 75%, and 100% (v/v) ethanol (for 15 min in each solvent). The membranes were dried in a critical point dryer (CPD) and sputtered with 5 nm Pt. Imaging was performed using a FEI Quanta 450 ESEM at 5 kV.

Atomic force microscopy (AFM) was used to study the nanostructure of self-associated collagen fibers. 0.5 mg of the collagen purified via Ni-NTA chromatography was re-solubilized in 1 mL of 1 mM phosphate buffer at pH=7.4. The collagen solution was incubated at 37° C. for 1 hour to facilitate the fibrillogenesis and self-association of the collagen fibrils. Then, 4 μL of the protein solution was added onto a freshly cleaved mica sheet, and was allowed to dry overnight. The samples were imaged using a Veeco Multimode Nanoscope III AFM with a 240AC-NA micro cantilever tip (Opus).

Circular Dichroism (CD) spectroscopy.

A Chirascan spectrophotometer (Applied Photophysics) was used to evaluate the secondary structure of the engineered proteins. Measurements were performed from 180 to 260 nm in a quartz cell with a 1-mm path length at 20° C., using 1 nm step size and a bandwidth of 1 nm. The protein solutions were prepared by dissolving 0.5 mg of the proteins in 1 mL of water, followed by 30 s vortexing to fully dissolve the proteins. All spectra were baseline corrected with respect to water.

Polarized Confocal Raman Spectroscopy.

Confocal Raman spectroscopy of the collagen samples were performed under dry conditions after spreading the samples onto glass slides. A green laser (Nd/YAG laser, λ=532 nm) was focused using a confocal Raman microscope equipped with a motorized scanning stage (Alpha300R, WItec, Ulm, Germany). The scattered light was detected by a thermoelectrically cooled CCD detector (Andor, Belfast, North Ireland) placed behind the spectrometer (WItec). Using a 100× objective (Zeiss, NA=0.9), individual point scans of vesicles contained large contributions from the surrounding glass and dried buffer; therefore, image scans were performed with laser power of 27 mW, polarization angles of 0° (perpendicular to major axis) and 90° (parallel to major axis), and integration time of 1.5 s per point.

Processing of Collagen Samples.

To test the potency of the collagen for being used in different forms for biomaterials applications, collagen was processed in the forms of free-standing films and hydrogel crosslinked with genipin, a naturally derived chemical crosslinker. To form the collagen films, a collagen solution (10 mg/mL) in 0.01 M acetic acid was incubated at 4° C. overnight, cast on glass slides, and air-dried overnight. An aqueous solution of collagen (1 mg/mL) was crosslinked by mixing with a solution of genipin (Abcam) in DMSO:PBS (1:3). Final concentrations of geninpin of 2.5 and 5 mM were used to compare the effect on mechanical properties. The collagen-genipin mixture was incubated at 37° C. overnight.

UV-vis analysis was used to confirm cross-linking by observing a characteristic absorption peak at 585 nm. Since genipin also endows the crosslinked proteins with an intrinsic fluorescence, the fluorescent properties of the genipin-crosslinked hydrogels were studied by a fluorometer (Thermo Fisher). The excitation wavelength was 590 nm and emission spectra were collected from 600 to 700 nm. In addition, rheological properties of the genipin-crosslinked collagen were studied using an Anton Paar MCR 302 rheometer.

Example VI Expression and Extracellular Secretion of Bacterial Collagen

To determine whether collagen was expressed and secreted extracellularly as expected through the curli secretion pathway, the presence of his-tagged collagen in the whole bacterial culture, in the supernatant only, and in the bacterial pellet only, was sought using SDS-PAGE and Western blotting (FIG. 8B). In the culture and supernatant, a band close to the expected molecular weight of bacterial collagen (˜34 kDa) was observed, which consisted of the N-terminal variable domain plus N22 (V′), translational enhancing element (TEE), His-tag, trypsin-sensitive region—for selective isolation of the collagen domain—, and collagen domain (CL) (FIG. 8B, lanes 1&2). This band was slightly higher (˜44 kDa) than the theoretical molecular weight of the construct, which is common for rod-like triple helix proteins. Meredith, S. C. The determination of molecular weight of proteins by gel permeation chromatography in organic solvents. Journal of Biological Chemistry 259, 11682-11685, (1984). The intensity of the band corresponding to the pellet was hard to distinguish (with an intensity of less than 1% of that of the whole culture), which indicates that the fraction of bacterial collagen that remains trapped inside the cells is negligible (FIG. 8B, lane 3). As expected, the intensity of the band for the supernatant was significantly higher (˜70% of intensity of the whole culture). Thus, after expression, a considerable fraction of the collagen (˜70%) is being secreted freely in the extracellular medium. The remaining fraction (˜30%), while not present in the washed pellet, may remain weakly associated with the pellet prior to washing with dilute hydrochloric acid and water. This extracellular, but pellet-associated collagen does not appear on the gels since the pellet that was run was washed. The supernatant may be used in subsequent purification processes and can readily allow to recover more than 70% of the expressed collagen. Notably, the curli secretion pathway is not specific to the secretion of CsgA proteins (Goyal, P. et al. Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG. Nature 516, 250-253, (2014); Van Gerven, N. et al. Secretion and functional display of fusion proteins through the curli biogenesis pathway. Mol Microbiol 91, 1022-1035, (2014)) and is instead compatible with the secretion of other proteins that are not CsgA, CsgA-like or fused to CsgA, such as collagen. Indeed, the N-terminal fusion of the Sec and N22 peptides was sufficient to ensure the efficient secretion of collagen.

The presence of assembled collagen was also confirmed in bacterial cultures after expression using SEM. FIG. 8C shows extracellularly secreted collagen (alongside an E. coli cell) and its fibrillar morphology, after self-associating into fiber meshwork in the bacterial culture. The presence of these self-assembled collagen fibers and aggregates directly in the bacterial culture suggests that collagen molecules begin forming fibrils and to bundle into networks immediately after expression and secretion.

To further visualize the secretion of triple-helical structures into the extracellular medium, the supernatant of cultures expressing collagen was stained using Sirius Red and Masson's trichrome dyes, and compared with cultures prepared with untransformed PQN4 cells (FIGS. 8D, 8E). Fibrillar collagen is highly anisotropic and forms a complex with Sirius Red that exhibits a strong birefringence, which can allow to distinguish collagen from non-collagenous proteins. Rittié, Methods Mol Biol Vol. 1627 Ch. 26, 395-407 (2017). The presence of basic amino acids in collagen makes the interaction with the dye stronger. Corrine, et al. A novel method for accurate collagen and biochemical assessment of pulmonary tissue utilizing one animal. Int J Clin Exp Pathol 4, 349-355 (2011). Under unpolarized light, stained fibrillar collagen is expected to appear red. Light microscopy of Sirius Red-stained samples revealed that untransformed PQN4 culture and the supernatant collected from collagen-secreting culture appeared orange and pink-red, respectively (FIG. 8D). Under polarized light, fibrillar collagen stained with Sirius Red is expected to appear in a range of colors, from yellowish-orange to orange-red. These colors were observed for the collagen-secreting culture only, and not for untransformed PQN4 cells, indicating the presence of extracellular collagen-like structures in PQN4 cells transformed with the pET21d-v′cl-csgCEFG (FIG. 8E). The area with the bright yellow/orange colour indicates larger and denser collagen fibers (FIG. 8E, top). Staining the samples with Masson's trichrome dye revealed similar information. With this method, collagen is expected to produce a blue color while other non-collagen components usually appear in red, pink, brown, and black. Lee, H. J. et al. Collagen mimetic peptide-conjugated photopolymerizable PEG hydrogel. Biomaterials 27, 5268-5276, (2006). The supernatant of a culture expressing collagen appeared intense blue after staining, compared with untransformed PQN4 cells, which appeared pink (FIG. 9). Together, these observations consistently indicate the presence of collagen in the extracellular medium of transformed cells.

Example VII Isolation of Secreted Collagen, and its Process-Dependent Morphology

Since collagen is secreted into the extracellular medium, its isolation does not require cell lysis, and collagen can be directly purified from the supernatant. After collecting the supernatant, collagen was isolated using three main methods: 1) affinity chromatography with Ni-NTA, along with two scalable methods, 2) size-based separation via crossflow filtration, and 3) collagen precipitation with phosphotungstic acid (PTA). These scalable methods can be preceded with a pepsin digestion step to digest protease-sensitive proteins in the supernatant and facilitate subsequent purification steps. They are then performed in a fairly quick manner, using simple size-based separation techniques (filtration and centrifugation). One liter of pepsin-digested supernatant could be purified in a 2 hour purification process with these methods. Notably, purification via precipitation also allows for considerably reducing the sample volume at an early stage in the process, from a large bacterial culture down to a few milliliters of product which can easily be lyophilized. Compared with the time that Ni-NTA purification takes (˜1 hour to purify 10 mL supernatant), this high productivity is an advantage for scalable manufacturing of biomaterials.

The purity and structure of the collagen products isolated from scalable methods was compared with those of collagen obtained from well-established Ni-NTA purification. After purification by the introduced three methods (FIG. 10A), the purity of the products using SDS-PAGE (FIG. 10B) was verified. The purity of the collagen samples obtained from pepsin digestion followed by precipitation (D-P) and from pepsin digestion followed by cross-flow filtration (D-CF) with the collagen obtained from Ni-NTA chromatography (V′CL/Ni) was compared. SDS-PAGE of the collected crude supernatant (without digestion or purification) showed a strong band for collagen with an initial approximate purity of 45%-50%. This relatively high initial purity in the crude supernatant is due to the fact that no cell lysis is needed for the extraction of collagen, preventing the release of intracellular proteins. This was observed for both collagens expressed in PQN4 cells and BL21 cells (FIG. 10B, lanes 1 & 2, respectively). In all of the digested samples, a band corresponding to the helical domain of bacterial collagen (CL domain) at around 23 kDa was observed (FIG. 10B, lanes 3, 4, 6, & 7). During the digestion step, the non-helical portions of the collagen construct, which are susceptible to protease digestion, were cleaved, while the helical domain (CL) remained intact with no cleavage or digestion during the purification process. After the pepsin digestion, the impurities' bands at higher and lower molecular weight than CL domain (23 kDa) were diminished and an intense band at around 12 kDa appeared, showing the digested impurities (FIG. 10B, lane 3). The purity of the collagen obtained from Ni-NTA (FIG. 10B, lane 5) was relatively higher than two other purification methods (FIG. 10B, lanes 4, 6, & 7) and showing no non-specifically bound impurities to the Ni-NTA column. To remove low molecular weight proteins after purification, centrifugal filters with 10 kDa or 30 kDa MWCO were employed. When a 10 kDa centrifugal filter was used, a band corresponding to the ˜22 kDa V′ fragment comprising N22, the non-helical domain, and the His-tag was still observed (FIG. 10B, lanes 4, 6). This band disappeared when a 30 kDa centrifugal filter was used (FIG. 10B, lane 7).

The purity of the collagen products obtained with each method was then compared and quantified. Ni-NTA yielded a collagen product with almost 100% purity, without any protein impurities visible on SDS-PAGE (FIG. 10B, lane 5), and with a ˜0.5 g/L yield. Indeed, this highly selectively Ni-NTA column allowed to retain only the his-tagged proteins (FIG. 11). In comparison, a purity of ˜90% for CL/D-CF samples was obtained when washed with 30 kDa filters (FIG. 10B, lane 7), with a yield of ˜0.4 g/L. While the yield for collagen purified via cross-flow filtration is comparable and even slightly lower than chromatography purification, cross-flow filtration is a technique that is more suitable for scale-up, could easily be adapted to isolate collagen for large culture volumes, and could be used in a continuous process. Finally, the purity of the CL/D-P sample was ˜60%, when washed with 10 kDa filter (FIG. 10B, lane 4). The lower molecular weight impurities could be removed by using 30 kDa filters. However, the lower yield for the latter (60 mg/L) was observed compared with the filtration method. This can be explained by the fact that acid precipitation does not result in the precipitation of all protein content in the supernatant, thus yielding less product. Although fewer protein impurities appeared in the collagen/Ni sample, tedious and time-consuming process, high cost, and trace of toxic Ni in the final purified product has been an enormous concern in the collagen-based biomaterials. Ueda, et. al. Current and prospective applications of metal ion-protein binding. Journal of Chromatography A 988, 1-23 (2003).

The morphology of collagen isolated with the three purification methods was compared via SEM (FIG. 10 (C-F)). V′CL/Ni samples showed nano-sized and micro-sized assembled fibrils (FIG. 10C). In some sections of the sample, collagen molecules that formed highly ordered networks with pore structures could also be recognize. For samples obtained via crossflow filtration, fibrillar structures and a meshwork of fibers could still be distinguished (FIG. 10D). However, when using the precipitation method, the fibrillar structure of the collagen appeared to have been affected by the acid treatment (FIG. 10E). The interaction of PTA with collagen molecules can rupture hydrogen bonds and electrostatic interactions throughout the collagen fibrils, therefore disordering its fibrillar structure. However, when adding erythritol as protecting agent during precipitation, the collagen structure was preserved against low pH (FIG. 10F). The presence of polyols can stabilize the triple helices by strengthening the bridge interaction between polypeptide chains and replacing the water molecules, thereby preserving hydrogen bonds within the collagen triple helix. Usha, et al. Role of polyols (erythritol, xylitol and sorbitol) on the structural stabilization of collagen. Chemical Physics Letters 430, 391-396, (2006). The preservation of the highly ordered fibrillar structure of collagen after purification is crucial in employing the final bacterial collagen product to design functional biomaterials. The biomimetic triple-helical fiber meshwork with porous structure obtained from isolated bacterial collagen makes this material a proper candidate for restorative biomaterials and tissue engineering applications, where cell integration and diffusion of nutrients are key parameters. Li, et al. Interpenetrating polymer networks of collagen, hyaluronic acid, and chondroitin sulfate as scaffolds for brain tissue engineering. Acta Biomater 112, 122-135, (2020).

Example VIII Structural Organization of Bacterial Collagen Proteins

Bacterial collagen triple helix formation and stability are mainly dependent on the electrostatic interactions between the charged amino acids, interactions of the polar residues between several GQN repeats, and the ordered hydration network involved in the numerous polar and charged residues in this domain. Mohs, A. et al. Mechanism of stabilization of a bacterial collagen triple helix in the absence of hydroxyproline. J Biol Chem 282, 29757-29765, doi:10.1074/jbc.M703991200 (2007). In bacterial collagen, 30% of the amino acids in the collagen domain are charged residues, which is 2-times more than the content of charged residues in type I animal collagen. Near the C-terminal end of bacterial collagen, a domain contains three full repeats of sequence GKD-GKD-GQN-GKD-GLP and several partial repeats of this sequence (FIG. 12A). Mohs, A. et al. Mechanism of stabilization of a bacterial collagen triple helix in the absence of hydroxyproline. J Biol Chem 282, 29757-29765, doi:10.1074/jbc.M703991200 (2007). The effect of charged residues, such as lysine (K) and aspartate (D), on the formation and stabilization of triple helix has been previously studied in collagen-like peptides. O'Leary, L. E., Fallas, J. A., Bakota, E. L., Kang, M. K. & Hartgerink, J. D. Multi-hierarchical self-assembly of a collagen mimetic peptide from triple helix to nanofibre and hydrogel. Nat Chem 3, 821-828, doi:10.1038/nchem.1123 (2011); Sarkar et al. Self-assembly of fiber-forming collagen mimetic peptides controlled by triple-helical nucleation. J Am Chem Soc 136, 14417-14424 (2014); Kohler, M. et al. Temperature-controlled electrospray ionization mass spectrometry as a tool to study collagen homo- and heterotrimers. Chem Sci 10, 9829-9835, (2019). Due to the formation of salt-bridged hydrogen bonds by K-D charge-pairs, these residues are sufficient to form a stable triple helix. In addition to the role of K-D charge-pairs at the C-terminal, there is a noticeable number of glutamate (E) and arginine (R) residues at the N-terminal of the collagen domain (FIG. 12A). Investigations in synthetic peptides have demonstrated that relatively stable triple helixes can be produced when these residues are found in the X and Y positions of the triplet (G-X-Y), respectively. Rele, et al. D-periodic collagen-mimetic microfibers. J. Am. Chem. Soc. 2007; 129:14780-14787. Therefore, the R-E pairs at the N-terminal of the collagen can favorably interact via electrostatic attractions and strengthen the triple helix formation throughout the collagen molecules. In a model suggested by Leary et al., (Sarkar et al. Self-assembly of fiber-forming collagen mimetic peptides controlled by triple-helical nucleation. J Am Chem Soc 136, 14417-14424 (2014)) it has been shown that a stable triple helix can be formed by the K-D charge-pairs, when the positively charged residue (K) at position X of the leading strand is paired with the negatively charged residue (D) at position Y of the middle strand, one triplet displaced toward the C-terminus. Similarly, the middle strand can interact with the lagging strand and the lagging strand can couple with the leading strand. FIG. 12B (top) shows the final assembled triple helix directed by K-D and R-E that forms a “blunt-end” triple helix, the model suggested by Leary et al. Sarkar et al. Self-assembly of fiber-forming collagen mimetic peptides controlled by triple-helical nucleation. J Am Chem Soc 136, 14417-14424 (2014); Tanrikulu, et al. Peptide tessellation yields micrometre-scale collagen triple helices. Nat Chem 8, 1008-1014, (2016)

Another possible interaction that could result in a different arrangement between the collagen molecules is the interaction between K and R (N-terminal end of one molecule with C-terminal end of another molecule). Hulgan et al., (Hulgan 2020) reported a faster formation of isopeptide bond between K and E compared with K-D pairs during self-assembly of the collagen mimetic peptides. Therefore, this potential electrostatic interaction can also direct the triple helix self-assembly, and eventually result in a “sticky-end” arrangement, another model suggested by Leary et al, (FIG. 12B, bottom). Sarkar et al. Self-assembly of fiber-forming collagen mimetic peptides controlled by triple-helical nucleation. J Am Chem Soc 136, 14417-14424 (2014); Tanrikulu, et al. Peptide tessellation yields micrometre-scale collagen triple helices. Nat Chem 8, 1008-1014, (2016). The possible sticky-end model in triple helix formation of the collagen can result in creation of overhangs that extend the length of the triple helix. Without being bound by theory, a single molecule of bacterial collagen is around 60 nm in length, which is 5 times shorter than type I animal collagen, and the suggested sticky-end arrangement for the bacterial collagen can result in indefinite triple helical elongation. Using AFM a collagen fiber that appeared to be around 45 nm thick and 400 nm long, as a result of triple helical elongation as well as lateral packing of the collagen molecules could be observed (FIG. 12C). A range of longer fibrils that bundled together also appeared on the AFM images. Furthermore, the extension can drive the fiber growth more extensively and form long uniform fibers, as observed by staining purified collagen fibers with Sirius Red (FIG. 12D). Upon Sirius Red staining, both animal collagen and bacterial collagen appeared orange-red under the polarized light. As mentioned previously, the binding of Sirius Red to the collagen backbone is an indication of triple helical structure. The presence of a stained collagen bundle of 50 μm in length and 3 μm in width confirms that the collagen molecules are capable of elongating and bundling into a population of nanofibers with triple helical packing similar to that of type I animal collagen. Animal collagen appeared as larger bundles compared with bacterial collagen, due to the larger size of the animal collagen molecule (˜1000 amino acids) compared with bacterial collagen (˜200 amino acids).

The formation of triple helical protein secondary structures in bacterial collagen after expression and purification using circular dichroism (CD) was also studied (FIG. 12E, 12F). The CD spectra of the V′CL/Ni at pH=7 showed a maximum value near 220 nm and a minimum near 200 nm (FIG. 12E). The positions of the maximum and minimum peaks demonstrate the characteristic spectrum of triple helical collagen similar to type I animal collagen, but with lower peak magnitudes, because of the smaller size of the bacterial collagen molecule. The CD spectrum of the V′CL showed a lower ellipticity at 220 compared with the isolated collagenous domain (CL), due to the presence of the helical non-collagenous domain (V′) in the V′CL sample (FIG. 12F).

The secondary structure of the collagen samples purified from scalable methods was also evaluated (FIG. 12E). The shape of the spectrum for CL/D-CF was similar to V′CL/Ni, but with lower ellipticity value at 220 nm, which could be due to a slight dissociation of the collagen molecules, potentially caused by the low pH necessary for the activity of the pepsin enzyme used in the digestion step (which precedes cross-flow filtration and precipitation purification, but not chromatography purification). More pronounced differences in the CL/D-P spectrum was observed. The positions and magnitude of the maximum and minimum peaks in the CL/D-P differed from V′CL/Ni. The pepsin and acid treatment may have caused the loss of triple helix structure and the emergence of a random coil (denatured) structure. Drzewiecki, et al. Circular Dichroism Spectroscopy of Collagen Fibrillogenesis: A New Use for an Old Technique. Biophys J 111, 2377-2386 (2016). Protecting the collagen with erythritol resulted in a less pronounced collagen denaturation, but an increase in its alpha helical content (trace at around 205 and 220 nm). This was in accordance with the SEM images of the protected and non-protected CL/D-P collagen, which showed fibril-like structures for protected collagen. The presence of erythritol molecules may have affected the assembly of the helical strands, and modified the collagen structure, from a triple-helix dominated structure to an alpha-helical one. The bacterial collagen sequence that was expressed can undergo this transition, due to the presence of charged amino acids and high proline content, which can be affected by low pH value.

To further investigate the role of the charged amino acid in the triple helix formation, the CD spectrum of the CL domain at pH=3 was obtained (FIG. 12F). To do so, the CL domain was first isolated via trypsin digestion. The ellipticity value significantly dropped at 220 nm when the resulting CL domain was exposed to acidic pH compared with pH=7. This reduction indicated that basic amino acids (aspartate and glutamate) play a significant role in triple helix formation for bacterial collagen, and that their electrostatic interactions can be disrupted in acidic pH.

To further investigate chemical and conformational changes of the collagen samples after the purification processes, the Raman spectra of the collagen samples was obtained. FIG. 12G shows the Raman spectra of the purified collagen molecules in the range of 1800-600 cm⁻¹, along with some relevant biomarkers and characteristic bands for type I collagen. In all bacterial collagen samples, there was a peak at around 1670 cm⁻¹ related to amide I vibration of the collagen, which comes from the carbonyl group of proline. Bands corresponding to carboxyl groups (aspartate and glutamate; around 1420 and 1100 cm⁻¹) and protonated amino residues (˜1150 cm⁻¹) were also observed. The vibrations at around 920 and 855 cm⁻¹ are assigned to the proline ring, reflecting the high proline content in bacterial collagen.

The amide III Raman band for proteins is located between 1210 to 1320 cm⁻¹. It typically consists of two major maxima at 1271 cm⁻¹ (assigned to nonpolar fragments with high proline content that form a typical collagen triple helix) and 1244 cm⁻¹ (assigned to polar fragments of collagen characterized by low proline content). Olsztynska-Janus et al. Spectroscopic techniques in the study of human tissues and their components. Part II: Raman spectroscopy. Acta of Bioengineering and Biomechanics 14, (2012). In the V′Cl/Ni sample, two peaks of the amide III region appeared at 1230 and 1270 cm⁻¹, as expected for type I collagen. Ikoma, Toshiyuki, Kobayashi, Hisatoshi, Tanaka, Junzo, Walsh, Dominic & Mann, Stephen. Physical properties of type I collagen extracted from fish scales of Pagrus major and Oreochromis niloticas. International Journal of Biological Macromolecules 32, 199-204, (2003). However, the amide III peaks have a lower intensity for CL/D-P compared with V′CL/Ni. Again, this structural difference is may be due to the effect of low pH during the precipitation process. The proline ring folding is significantly influenced by the environment. In particular, changes in pH values alter chirality of the proline (by affecting the bond lengths and angle between bonding atoms) (Qiu, S. et al. pH-dependent chirality of L-proline studied by Raman optical activity and density functional theory calculation. J Phys Chem A 115, 1340-1349, doi:10.1021/jp111631a (2011); Tellez Soto, C. A. et al. DFT:B3LYP/3-21G theoretical insights on the confocal Raman experimental observations in skin dermis of healthy young, healthy elderly, and diabetic elderly women. J Biomed Opt 21, 125002, (2016)) and vibration of the N—H bending. Nevertheless, upon protection by erythritol and in the CL/D-CF sample, a more intense peak at around 1250 cm⁻¹ became visible, which could be due to the effect of low pH on the N—H bending vibration.

From CD and Raman investigations, the collagen obtained from Ni-NTA chromatography forms ordered triple helical structures, and the collagen purified via crossflow filtration or acid precipitation is slightly more disordered. The acidic processing steps (starting with pepsin digestion) may disrupt some of the interactions between collagen chains. It may be possible, however, to modify the purification processes to avoid compromising triple helix formation, by omitting the pepsin digestion step, and by protecting collagen against acids with erythritol.

Example IX Processing Bacterial Collagen

The secreted and purified collagen could be used to fabricate materials, as observed by the processability of the collagen samples. Samples were formulated into thin films and crosslinked hydrogels. First, freeze-dried collagen samples showed a sponge-like fibrous structure that could mimic the fibrous structure of type I collagen (FIG. 13A, top). Next, free-standing thin films of ˜0.2 mm thickness were prepared by casting the collagen solution into silicon molds (FIG. 13A, bottom). Such films could be applied to wound healing and tissue engineering problems. Chattopadhyay, S. & Raines, R. T. Review collagen-based biomaterials for wound healing. Biopolymers 101, 821-833, doi:10.1002/bip.22486 (2014). Since collagen possesses high biodegradability and morphological plasticity, it is capable of rebuilding the microenvironment of wounded tissues and achieve infiltration of a variety of cells, neovascularization, and extracellular matrix deposition. Long, G. et al. A dual functional collagen scaffold coordinates angiogenesis and inflammation for diabetic wound healing. Biomater Sci 8, 6337-6349.

Although collagen holds valued biochemical properties such as resistance to protease degradation, it requires physical or chemical modifications to improve its stability especially for in vivo applications. Genipin was used to crosslink the collagen samples. Genipin can react with the primary amine groups of the collagen and form cyclic structures that act as fluorophores. To confirm the successful genipin crosslinking reaction, the absorbance and fluorescence of the crosslinked collagen materials was measured. In the presence of oxygen, genipin-bound amines turn blue and their absorbance at ˜590 nm increases (FIG. 13C). The genipin-modified collagen fluoresces at ˜640 nm (FIG. 13D). Increased absorbance and fluorescence intensities with increasing genipin to collagen ratio was observed, yielding more crosslink points. To investigate the effect of the crosslinking on collagen strength, the storage modulus of the crosslinked and non-crosslinked samples was measured. Upon crosslinking, strong chemical bonds between collagen molecules can be formed that strengthen the intramolecular and intermolecular interactions between them. This interaction can increase the collagen strength and stability. Macaya, et al. Injectable Collagen-Genipin Gel for the Treatment of Spinal Cord Injury: In Vitro Studies. Adv. Funct. Mater. 21, 4788-4797 (2011).

Bacterial collagen possesses structural stability and features (triple helix) comparable to type I animal collagen with emerging uses as biomaterials for a broad range of applications. Herein, the extracellular secretion system for curli fibers was modified resulting in an efficient secretion pathway for bacterial collagen in E. coli cells. The extracellular secretion prevented the need for cell rupture, and therefore, simplified the isolation of bacterial collagen. After simply centrifuging the bacterial culture after expression, the crude supernatant itself exhibited a close to 50% collagen content. Then, using cost-effective and simple purification methods, more than 80% purity and around 0.4 g/L purification yield could be obtained, in a fast and easy manner.

Analysis of the morphology and secondary structure of the collagen products indicated that the secreted and purified bacterial collagen formed triple helical fibrous structures. While the structure of bacterial collagen differs slightly from type I collagen, as it is held together by pairs of charged residues, they share many structural and physicochemical characteristics. Secreted bacterial collagen could form elongated triple-helical structures of hundreds of nanomaterials in length, held together by electrostatic interactions. Moreover, bacterial collagen can be processed as dried proteins, films, and cross-linked hydrogels, all of which can enable the utilization of collagen as a main component of functional biomaterials.

REFERENCES

Each of the following references is hereby incorporated by reference in its entirety:

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INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned herein are hereby incorporated by reference in their entirety as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims. 

1. A method of producing a genetically modified bacterium, comprising genetically altering a bacterium to include a nucleic acid sequence encoding recombinant polypeptide comprising a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and one or more bacterial collagen domains, wherein the nucleic acid is under operation of a promoter to express the recombinant protein.
 2. A method of purifying bacterial collagen, comprising proliferating a genetically-altered bacterium comprising a nucleic acid sequence encoding recombinant polypeptide comprising a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and one or more bacterial collagen domains, to produce a population of genetically-altered bacteria expressing the nucleic acid sequence, allowing the bacteria to secrete the bacterial collagen into the extracellular medium, and isolating the bacterial collagen from the extracellular medium.
 3. The method of claim 2, wherein isolating the bacterial collagen from the extracellular medium comprises nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography.
 4. The method of claim 3, wherein the bacterial collagen further comprises a histidine (HIS) tag.
 5. The method of claim 2, wherein isolating the bacterial collagen from the extracellular medium comprises size-based separation via crossflow filtration.
 6. The method of claim 5, wherein prior to size-based separation via crossflow filtration the extracellular medium is digested with pepsin.
 7. The method of claim 5, comprising crossflow filtration through a 10 kDa molecular weight cut-off (MWCO) membrane, wherein the solutes and digested proteins are isolated in the permeate and the bacterial collagen is isolated in the retentate.
 8. The method of claim 2, wherein isolating the bacterial collagen from the extracellular medium comprises acid precipitation.
 9. The method of claim 8, wherein prior to acid precipitation the extracellular medium is digested with pepsin.
 10. The method of claim 8, wherein protein is precipitated with phosphotungstic acid (PTA).
 11. The method of claim 8, wherein the acid precipitation further comprises erythritol.
 12. A method of making a collagen biofilm, comprising proliferating a genetically-altered bacterium comprising a nucleic acid sequence encoding recombinant polypeptide comprising a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion and one or more bacterial collagen domains, allowing the bacteria to secrete the bacterial collagen into the extracellular medium to form a biofilm comprising a triple-helical collagen based structure, wherein the triple-helical collagen based structure is deposited on a substrate.
 13. The method of claim 12, further comprising physical or chemical modification of the collagen to improve stability. 14-15. (canceled)
 16. The method of claim 1, wherein the domain for directing the recombinant protein to the outer membrane for secretion is an N22 domain.
 17. The method of claim 1, wherein the domain for periplasmic localization is a Sec domain.
 18. (canceled)
 19. The method of claim 1, wherein the one or more bacterial collagen domains comprise a variable domain (V′), an intervening trypsin-sensitive region, and a collagen domain (CL).
 20. The method of claim 1, wherein the recombinant polypeptide further comprises a translational enhancing element (TEE).
 21. (canceled)
 22. The method of claim 1, wherein the nucleic acid sequence further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG.
 23. The method of claim 1, wherein the bacterium is E. coli.
 24. (canceled)
 25. A genetically-modified bacterium, comprising a nucleic acid sequence encoding recombinant polypeptide comprising a domain for periplasmic localization, a domain for directing the recombinant protein to the outer membrane for secretion, and one or more bacterial collagen domains, wherein the nucleic acid sequence is under the control of a promoter to express the recombinant polypeptide.
 26. The genetically-modified bacterium of claim 25, wherein the domain for directing the recombinant polypeptide to the outer membrane for secretion is an N22 domain.
 27. The genetically-modified bacterium of claim 25, wherein the domain for periplasmic localization is a Sec domain.
 28. (canceled)
 29. The genetically-modified bacterium of claim 25, wherein the one or more bacterial collagen domains comprise a variable domain (V′), an intervening trypsin-sensitive region, and a collagen domain (CL).
 30. The genetically-modified bacterium of claim 25, wherein the recombinant polypeptide further comprises a translational enhancing element (TEE).
 31. (canceled)
 32. The genetically-modified bacterium of claim 25, wherein the nucleic acid sequence further encodes each of the curli-specific accessory proteins selected from csgC, csgE, csgF, and csgG.
 33. The genetically-modified bacterium of claim 25, wherein the bacterium is E. coli.
 34. (canceled)
 35. A non-naturally occurring bacterial collagen polypeptide, comprising the sequence set forth in SEQ ID NO:
 207. 36-40. (canceled)
 41. A nucleic acid sequence encoding the non-naturally occurring bacterial collagen polypeptide of claim
 35. 42. A vector, comprising the nucleic acid sequence of claim
 41. 43-45. (canceled) 